It's the fourth time this year that crew members on Indonesian boats travelling through essential trade routes in Philippine waters have been set upon by armed militant groups and taken hostage.
This week, in two separate incidents on Monday, 13 people were taken from two boats, prompting the Indonesian government to renew calls on the Philippines government to secure its seas.
Six Indonesians have been released but a further seven remain captive.
"The Indonesian government strongly condemns this repeated hostage taking of Indonesians by armed groups in the southern Philippines," Foreign Minister Retno Marsudi told reporters on Friday.
"The Indonesian government asks the Philippine government to ensure the safety of southern Philippine waters so that there is no disturbances in economic activity."
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While the foreign ministry has yet to confirm, it says it is "possible" the Abu Sayyaf group was again behind the kidnappings.
Abu Sayyaf is known for its kidnap-for-ransom and extortion ventures, the former being its main source of funding since its creation in 1991.
Earlier this month Robert Hall, a Canadian national, was beheaded by the group after being held for nine months.
Meanwhile, 14 Indonesians were taken hostage in two incidents in March and April while shipping coal through the region.
After intensive negotiations involving "informal" and "formal" avenues the crew were released.
But the militant group's ongoing activities in the region have stirred up concerns the essential shipping route in the Sulu Sea could become a "new Somalia".
Last week Indonesia's Defence Minister Ryamizard Ryacudu said maritime security and terrorism posed the two greatest threats to the archipelago's security and that the governments needed to "intensify" regional collaboration.
The two countries, as well as Malaysia, have discussing operating joint patrols in the region.
Indonesia's national counter-terrorism agency (BNPT) chief Tito Karnavian said on Thursday night Indonesia hoped to hold further talks with the Philippines in August on increasing co-operation between intelligence units.
Meanwhile, Philippine President Rodrigo Duterte said this week he needed more time to address terrorism in the country but warned the Abu Sayyaf group it would have to face the consequences of its actions soon.
