According to MANA, Nearly 20 Indonesian and Malaysian tugboat crew have been kidnapped by militants this year, with Jakarta airing fears that the problem could reach levels seen off the coast of Somalia.
Alarmed at the frequency of attacks, port authorities in some areas of Indonesia, particularly Kalimantan on the island of Borneo, have stopped issuing permits to ships taking coal to the southern Philippines.
"The ministers have agreed in principle to explore the following measures, including a transit corridor within the maritime areas of common concern, which will serve as designated sea lanes for mariners," the defence ministers of the three nations said in a joint statement after a meeting in Manila.
Analysts say $40bn worth of cargo passes through the Sulu and Celebes seas each year, including supertankers from the Indian Ocean that cannot use the crowded Malacca Strait.
The three countries also agreed to step up air and sea patrols and escorts for commercial ships in the common maritime areas to fend off potential hijacks, kidnaps and robbery.
Philippine Defence Secretary Voltaire Gazmin said the leaders agreed to share the best practices evolved by Indonesia and Malaysia during a joint effort to patrol the busy Malacca Strait waterway against pirates, as a model for three-way cooperation with the Philippines.
In 2002, Indonesia, Malaysia and the Philippines, which share maritime borders, signed a pact to stiffen security against growing cross-border attacks.
But they have not set up coordinated naval patrols, with navies operating in their own territorial waters.