Four Indonesian crew members were abducted on Friday evening in another incident on the seas.
It is not known whether the abductors are from the Abu Sayyaf group which has been holding 10 Indonesian sailors hostage since last March.
"We are still doing an analysis. We do not know for sure who is holding them hostage. We are studying the motive of the abductors, whether it is political or purely for money such as those in Somalia," Pandjaitan said here, Saturday when attending a ceremony celebrating the 64th anniversary of the Indonesian Armys Special Force, Kopassus.
A negotiation between the Abu Sayyaf group and the sailors companies to release the 10 hostages is still going on, he said.
The government is still awaiting the results of that negotiation, he said.
The Commander of the Indonesian Defense Forces (TNI), General Gatot Nurmantyo, however, said that the four Indonesian crew members are most likely being held hostage by the Abu Sayyaf group.
"There are some 10 Indonesians in the boats. Four are being held hostage, while six others survived and are currently being secured in Sabah, Malaysia," he said.
Of the six, one was shot and is currently being treated in Malaysia.
The TNI has deployed two warships, KRI Badau and KRI Slamet Riyadi, in the Indonesian waters that share maritime borders with Malaysia and the Philippines.
The government will explore cooperation to secure the waters with the governments of Malaysia and the Philippines, he said.
Earlier, the Indonesian foreign ministry reported that two Indonesia-flagged boats, TB Henry and Barge Christi, were hijacked in the maritime border of Malaysia and the Philippines Friday.
The two boats were on their way from Cebu, the Philippines, to Tarakan, North Kalimantan, when the hijacking occurred, the Indonesian foreign affairs ministry said in a statement.
The hijacked boats carried 10 Indonesian crew members. Of the 10, one was shot, five managed to escape, and four were abducted by the pirates.
The injured crew member was rescued by Malaysian Maritime Police and taken to Malaysia for medical treatment. He is in stable condition, according to the ministry.
The five survivors and the two boats were also taken by the Malaysian police to Lahat Datu seaport, Malaysia.
In an earlier incident, 10 Indonesian sailors were kidnapped by the Abu Sayyaf group in waters near the Philippines, on March 28, 2016.
The Abu Sayyaf group has demanded a 50 million peso ransom, or about Rp14.2 billion. The negotiations for their release is still going on.(*)