The owner of the hijacked tug boat and coal barge has received two telephone calls, allegedly from the Abu Sayyaf group, demanding a ransom.
Indonesia's foreign ministry said it was not known when the hijacking took place but that the ship owner was first contacted on Saturday. The ministry also referred to the hijackers as pirates.
The tug, Brahma 12, and the Anand 12 barge were going from Sungai Putting in Kalimantan, which is the Indonesian part of Borneo island, to Batangas in the southern Philippines. The crew was able to call their employer to report the hijacking but their whereabouts remain unknown.
Abu Sayyaf is on the US and Philippine list of terrorist organizations. The al-Qaeda-linked group has carried out bombings, extortions and kidnappings for ransom in the south of the Philippines. It is one of the most hardline Islamist militant groups in the Muslim south of the largely Christian Philippines.
Last year, two Canadians, a Norwegian and a Filipino woman were abducted from a marina on Samal Island.