Indonesia has called for increased sea security in the region, after 10 crew were released by Abu Sayyaf militants following a month-long hostage ordeal.
Indonesian President Joko "Jokowi" Widodo thanked the Philippines government for their cooperation on Sunday in helping secure the release of the Indonesians who were taken by the Islamic rebels while travelling in southern Philippine waters in March.
It is understood the group called for a ransom of 50 million Philippine peso ($A1.42 million) for the men but it is not known if any money was handed over.
Jokowi said they were still working hard to release another four Indonesians captured by the group in a separate incident on April 15 while also in Philippine waters.
But he said attention must also be given to the security of the waters in the region, with a meeting this week between Indonesia, Malaysia and the Philippines slated to discuss increased security.
Security Minister Luhut Panjaitan has previously expressed concerns Indonesia did not want the popular shipping route in the Sulu Sea to become a "new Somalia",
It is expected foreign ministers and military chiefs from Malaysia, the Philippines and Indonesia will discuss the possibility of joint patrols.
The Abu Sayyaf group is known for its kidnap-for-ransom and extortion ventures, with the former being its main source of funding since its creation in 1991.
Just last week 68-year-old Canadian John Ridsdel was executed by the group, who captured the former mining executive and three others last year while they were holidaying on a Philippine island.
The Indonesian vessels - tugboat Brahma 12 and barge Anand 12 - were shipping coal from South Kalimantan to Batangas in the southern Philippines when they were captured.
Indonesian Foreign Minister Retno Marsudi said a "lot of parties" were involved in securing their release, including "informal networks".
They men are expected to undergo health checks on Monday.
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