Indonesia, Malaysia and the Philippines would meet on Thursday (May 5) in Yogyakarta to discuss regional security, with joint patrols in the Sulu and Sulawesi Seas top of the agenda.
The recent spate of kidnappings in the region has increased the need for security, with ship owners urged to take preventive measures.
"Firstly, (ship owners) should do a 'double watch', which means they must have crew watching the front and back of the vessel when travelling through dangerous areas," said Budhi Halim, Secretary-General of the Indonesian National Shipowners Association.
"Secondly, they must move in a convoy, don't travel alone. If they are two or three vessels, they can travel together."
Indonesia, the Philippines and Malaysia are considering the possibility of conducting joint patrols in both seas, but many vessels are turning to their own security measures, with some embedding armed security personnel to deter pirates.
"That's a good solution," said Hanafi Rustandi, Chairman of the International Transport Workers' Federation.
"Embedding armed security personnel is important. Usually the Abu Sayyaf, the hijackers use small boats which can fit only four to five people, and the armed guards will be able to deal with them."
These armed guards are former members of the navy or military, with smaller vessels usually deploying one or two of them.
However, higher costs and extra insurance premiums have deterred some shipping companies from using them.
"For shipowners, the issue is about cost, you need more cost for this kind of embedded security guards," said Alman Helvas Ali, Researcher at the Indonesian Insititute for Defense and Strategic Studies.
Indonesian vessels are however protected to some extent, with the Indonesian Shipowners Association having a protection and indemnity fund to cover areas that fall outside normal insurance coverage, including ransom money paid to hijackers and kidnappers.