12 November 2025
IP25106 | Maritime Security in the Southern Philippines: Building Upon Gains Amid Evolving Threats
KEY TAKEAWAYS
• The maritime security situation in the southern Philippines and neighbouring areas of Malaysia and Indonesia has greatly improved in recent years, thanks to coordinated government action.
• The threats from terrorism and kidnapping have been reduced, but other forms of maritime criminal activity have become even more prominent, with smuggling and human trafficking emerging as the foremost concerns.
• The Philippines, its neighbours, and its partners should leverage the positive momentum to build upon the gains, rather than shifting resources away.
COMMENTARY
The Bangsamoro peace process in the southern Philippines has travelled a rocky road in the decade since the agreement was signed between the national government and the area’s largest armed group, the Moro Islamic Liberation Front (MILF), in 2014. In October 2025, a series of court cases that derailed the first elections in the Bangsamoro Autonomous Region in Muslim Mindanao presented the latest bump – possibly a very consequential one. However, in the same decade, the maritime security situation has significantly improved in this area’s seas, which, as a matter of geography, history, and culture, are directly linked to the larger Philippines–Malaysia–Indonesia tri-border area (TBA).
A decade ago, the waters around the TBA were awash with banditry. The kidnapping of mariners and coastal residents was one of the most lucrative forms of crime. When eleven kidnapping incidents (nine successful) were documented over a nine-month period during 2016, alarm bells rang in the shipping community.
The cresting waves of maritime violence prompted Indonesia, Malaysia and the Philippines to begin coordinating air and maritime patrols under the auspices of the 2017 Trilateral Cooperative Arrangement. Since then, the Philippine government has arrested hundreds of suspects and engaged in clashes with members of maritime-savvy armed organisations, while also focusing on the region’s economic development. There have been no incidents of kidnapping at sea since January 2020.
Given the range of intense challenges the three nations face – especially in the maritime domain – it is both natural and appropriate that they may reorient resources towards other priorities. However, it would be a mistake to rest on their laurels. While the violence may have lessened, the TBA waters are still plagued by crime. It would be wiser to continue building on this success rather than easing the pressure, thereby allowing the criminals to reconstitute.
Maritime Threats Persist in Complex Maritime Geography
While the threats from terrorism and kidnapping have been reduced, they have not been eliminated, and other forms of maritime criminal activity have become even more prominent. Drug trafficking; human trafficking; illegal, unreported and unregulated (IUU) fishing; and the smuggling of trade goods such as oil, cigarettes, rice and even onions, are among the concerns.
The Zamboanga Peninsula serves as a major hub for these illicit activities and a gateway between key markets in the southern Philippines. Sulu and Tawi-Tawi are well-known transhipment points – stepping stones to Semporna and Sandakan on the Sabah coast and to the Indonesian ports of Nunukan and Tarakan. Ethnic Tausug and Sama seafarers are often involved, but it is incorrect to place the blame on them. Mariners of other ethnicities are also involved, and the routes cannot function without the shore-based sourcing and distributing networks.
According to a recent report by the United Nations Office on Drugs and Crime (UNODC), the area has become an increasingly busy hub for the movement of illegal drugs from Myanmar to the Philippines and eastern Indonesia, Australia, and the Pacific. According to the Philippines Drug Enforcement Agency, a single drug trafficking syndicate – the Upik Gang – transports approximately two tonnes of crystal methamphetamine annually along this route. In addition, the southern Philippines is emerging as a methamphetamine production and export centre.
Human trafficking is another persistent peril in the region. While many of those trafficked go voluntarily – following legitimate work and cultural movement patterns but lacking the appropriate paperwork – some are lured by false promises of jobs in palm oil plantations and logging industries. Others are being forcibly moved against their will, with women and minors particularly at risk. The primary driver of this phenomenon is insufficient economic opportunity in the southern Philippines. A major route is the so-called “Southern Backdoor” into Malaysia.
Oil tends to flow in the opposite direction, finding its way from Kota Kinabalu to Tawi-Tawi and Zamboanga. The Philippine Coast Guard’s (PCG) 2023 apprehension of two vessels (one Malaysian, the other Philippine) transferring 400,000 litres of gasoline worth around US$500,000 illustrates the modus operandi. In some documented cases, fuel smuggling and human trafficking were linked with ship-to-ship transfers used to evade law enforcement.
Cigarette smuggling is another common cross-border maritime crime. A single motor launch can carry more than US$1 million worth of foreign cigarettes to Philippine markets. Smuggled cigarettes can cost as little as a third of the price of regulated ones, and cigarette smuggling has been estimated to cost the Philippine government as much as US$1 billion in revenue per year while undermining local farmers and brands. These cigarettes are also more accessible to young people, increasing public health risks. Similar market-driven dynamics are at play in petroleum smuggling.
Looking ahead, gun smuggling could likewise occur through entrenched smuggling networks, as clandestine manufacturers and holders of unregistered firearms seek new markets.
Proven Enforcement Methods
The TBA’s hundreds of islands and mobile populations of highly skilled mariners present formidable geography for law enforcement. This environment limits the effectiveness of land-based personnel and radars, while governments face common shortfalls in airborne and floating assets. Yet, the authorities have proven tools at their disposal.
Inter-agency cooperation frameworks are effective options to strengthen government action and bring high-value capabilities to bear. In Malaysia, the Eastern Sabah Security Command puts forces from the police, armed forces, Malaysian Maritime Enforcement Agency, and other agencies under a centralised authority, and has proven quite effective. In the Philippines, a network of inter-agency task forces, memoranda of understanding (MOUs), coordination meetings, and joint training exercises is in place, with opportunities to further strengthen cooperation between agencies and international partners actively being pursued.
Cooperation with local populations has also improved, becoming a key strength of government efforts. In the Philippines, provincial intelligence units and the township-level Barangay Intelligence Network personnel have been key to identifying perpetrators and guiding maritime patrols. Enforcing the registration of all small craft has been labour-intensive, but simple and tremendously effective.
Finally, international partnerships have been key to empowering maritime governance in the Philippines. The coordinated at-sea patrols and other activities with Malaysia and Indonesia are at the core, but extra-regional partners also played an important role. Japanese assistance – including the provision of patrol craft – has been crucial to expanding PCG capacity. Support from the European Union’s Governance in Justice Programme, the ASEAN–Australia Counter Trafficking partnership, the US Agency for International Development (USAID), the UNODC, and others has expanded local capacity.
Charting the Course Forward
The Philippines needs to improve its “legal finish” to ensure apprehension, prosecution and punishment are better linked to strengthen deterrence. For example, prosecutor hands have been strengthened by the categorisation of tobacco smuggling as an act of economic sabotage (under House Bill 3917 and Senate Bill 1812), which carries a sentence of 20 to 40 years’ imprisonment, and by the creation of a special court for smuggling (Senate Bill 1963) with a compulsory clause holding the Bureau of Customs and Department of Justice (DOJ) liable for any “refusal to prosecute large scale agricultural smuggling”. However, while apprehensions are reported in the media, data on convictions remain unavailable.
The Philippines should continue to seek international support and partnership. The reprioritisation of US foreign assistance has already had a negative impact, with the dismantling of the USAID and the sudden termination of valuable activities being previously implemented by the US Institute for Peace. These gaps must be plugged both to assist with the larger peace and reconciliation process, but also to cement the progress that has been achieved at sea and to counter persistent maritime threats. Luckily, the Philippines is not alone. A broad range of partners understand that maritime insecurity in the southern Philippines is not an issue that is contained by borders, and that improved conditions there will allow the national government to more comfortably allocate additional resources to face other challenges.
John F. Bradford is an Adjunct Senior Fellow in the Maritime Security Programme at the S Rajaratnam School of International Studies (RSIS). Aaron Jed Rabena is an Assistant Professor at the Asian Center in the University of the Philippines.
KEY TAKEAWAYS
• The maritime security situation in the southern Philippines and neighbouring areas of Malaysia and Indonesia has greatly improved in recent years, thanks to coordinated government action.
• The threats from terrorism and kidnapping have been reduced, but other forms of maritime criminal activity have become even more prominent, with smuggling and human trafficking emerging as the foremost concerns.
• The Philippines, its neighbours, and its partners should leverage the positive momentum to build upon the gains, rather than shifting resources away.
COMMENTARY
The Bangsamoro peace process in the southern Philippines has travelled a rocky road in the decade since the agreement was signed between the national government and the area’s largest armed group, the Moro Islamic Liberation Front (MILF), in 2014. In October 2025, a series of court cases that derailed the first elections in the Bangsamoro Autonomous Region in Muslim Mindanao presented the latest bump – possibly a very consequential one. However, in the same decade, the maritime security situation has significantly improved in this area’s seas, which, as a matter of geography, history, and culture, are directly linked to the larger Philippines–Malaysia–Indonesia tri-border area (TBA).
A decade ago, the waters around the TBA were awash with banditry. The kidnapping of mariners and coastal residents was one of the most lucrative forms of crime. When eleven kidnapping incidents (nine successful) were documented over a nine-month period during 2016, alarm bells rang in the shipping community.
The cresting waves of maritime violence prompted Indonesia, Malaysia and the Philippines to begin coordinating air and maritime patrols under the auspices of the 2017 Trilateral Cooperative Arrangement. Since then, the Philippine government has arrested hundreds of suspects and engaged in clashes with members of maritime-savvy armed organisations, while also focusing on the region’s economic development. There have been no incidents of kidnapping at sea since January 2020.
Given the range of intense challenges the three nations face – especially in the maritime domain – it is both natural and appropriate that they may reorient resources towards other priorities. However, it would be a mistake to rest on their laurels. While the violence may have lessened, the TBA waters are still plagued by crime. It would be wiser to continue building on this success rather than easing the pressure, thereby allowing the criminals to reconstitute.
Maritime Threats Persist in Complex Maritime Geography
While the threats from terrorism and kidnapping have been reduced, they have not been eliminated, and other forms of maritime criminal activity have become even more prominent. Drug trafficking; human trafficking; illegal, unreported and unregulated (IUU) fishing; and the smuggling of trade goods such as oil, cigarettes, rice and even onions, are among the concerns.
The Zamboanga Peninsula serves as a major hub for these illicit activities and a gateway between key markets in the southern Philippines. Sulu and Tawi-Tawi are well-known transhipment points – stepping stones to Semporna and Sandakan on the Sabah coast and to the Indonesian ports of Nunukan and Tarakan. Ethnic Tausug and Sama seafarers are often involved, but it is incorrect to place the blame on them. Mariners of other ethnicities are also involved, and the routes cannot function without the shore-based sourcing and distributing networks.
According to a recent report by the United Nations Office on Drugs and Crime (UNODC), the area has become an increasingly busy hub for the movement of illegal drugs from Myanmar to the Philippines and eastern Indonesia, Australia, and the Pacific. According to the Philippines Drug Enforcement Agency, a single drug trafficking syndicate – the Upik Gang – transports approximately two tonnes of crystal methamphetamine annually along this route. In addition, the southern Philippines is emerging as a methamphetamine production and export centre.
Human trafficking is another persistent peril in the region. While many of those trafficked go voluntarily – following legitimate work and cultural movement patterns but lacking the appropriate paperwork – some are lured by false promises of jobs in palm oil plantations and logging industries. Others are being forcibly moved against their will, with women and minors particularly at risk. The primary driver of this phenomenon is insufficient economic opportunity in the southern Philippines. A major route is the so-called “Southern Backdoor” into Malaysia.
Oil tends to flow in the opposite direction, finding its way from Kota Kinabalu to Tawi-Tawi and Zamboanga. The Philippine Coast Guard’s (PCG) 2023 apprehension of two vessels (one Malaysian, the other Philippine) transferring 400,000 litres of gasoline worth around US$500,000 illustrates the modus operandi. In some documented cases, fuel smuggling and human trafficking were linked with ship-to-ship transfers used to evade law enforcement.
Cigarette smuggling is another common cross-border maritime crime. A single motor launch can carry more than US$1 million worth of foreign cigarettes to Philippine markets. Smuggled cigarettes can cost as little as a third of the price of regulated ones, and cigarette smuggling has been estimated to cost the Philippine government as much as US$1 billion in revenue per year while undermining local farmers and brands. These cigarettes are also more accessible to young people, increasing public health risks. Similar market-driven dynamics are at play in petroleum smuggling.
Looking ahead, gun smuggling could likewise occur through entrenched smuggling networks, as clandestine manufacturers and holders of unregistered firearms seek new markets.
Proven Enforcement Methods
The TBA’s hundreds of islands and mobile populations of highly skilled mariners present formidable geography for law enforcement. This environment limits the effectiveness of land-based personnel and radars, while governments face common shortfalls in airborne and floating assets. Yet, the authorities have proven tools at their disposal.
Inter-agency cooperation frameworks are effective options to strengthen government action and bring high-value capabilities to bear. In Malaysia, the Eastern Sabah Security Command puts forces from the police, armed forces, Malaysian Maritime Enforcement Agency, and other agencies under a centralised authority, and has proven quite effective. In the Philippines, a network of inter-agency task forces, memoranda of understanding (MOUs), coordination meetings, and joint training exercises is in place, with opportunities to further strengthen cooperation between agencies and international partners actively being pursued.
Cooperation with local populations has also improved, becoming a key strength of government efforts. In the Philippines, provincial intelligence units and the township-level Barangay Intelligence Network personnel have been key to identifying perpetrators and guiding maritime patrols. Enforcing the registration of all small craft has been labour-intensive, but simple and tremendously effective.
Finally, international partnerships have been key to empowering maritime governance in the Philippines. The coordinated at-sea patrols and other activities with Malaysia and Indonesia are at the core, but extra-regional partners also played an important role. Japanese assistance – including the provision of patrol craft – has been crucial to expanding PCG capacity. Support from the European Union’s Governance in Justice Programme, the ASEAN–Australia Counter Trafficking partnership, the US Agency for International Development (USAID), the UNODC, and others has expanded local capacity.
Charting the Course Forward
The Philippines needs to improve its “legal finish” to ensure apprehension, prosecution and punishment are better linked to strengthen deterrence. For example, prosecutor hands have been strengthened by the categorisation of tobacco smuggling as an act of economic sabotage (under House Bill 3917 and Senate Bill 1812), which carries a sentence of 20 to 40 years’ imprisonment, and by the creation of a special court for smuggling (Senate Bill 1963) with a compulsory clause holding the Bureau of Customs and Department of Justice (DOJ) liable for any “refusal to prosecute large scale agricultural smuggling”. However, while apprehensions are reported in the media, data on convictions remain unavailable.
The Philippines should continue to seek international support and partnership. The reprioritisation of US foreign assistance has already had a negative impact, with the dismantling of the USAID and the sudden termination of valuable activities being previously implemented by the US Institute for Peace. These gaps must be plugged both to assist with the larger peace and reconciliation process, but also to cement the progress that has been achieved at sea and to counter persistent maritime threats. Luckily, the Philippines is not alone. A broad range of partners understand that maritime insecurity in the southern Philippines is not an issue that is contained by borders, and that improved conditions there will allow the national government to more comfortably allocate additional resources to face other challenges.
John F. Bradford is an Adjunct Senior Fellow in the Maritime Security Programme at the S Rajaratnam School of International Studies (RSIS). Aaron Jed Rabena is an Assistant Professor at the Asian Center in the University of the Philippines.
