The 10 crew members were abducted from the Brahma 12 tugboat and the Anand 12 barge -- carrying 7,000 tons of coal -- in recent days near the country's southernmost Tawi-Tawi province, according to Indonesian Foreign Minister Retno Marsudi.
The ship owners learned of the hijacking Saturday when a person claiming to be a member of the Abu Sayyaf Islamist group called to demand a ransom, Marsudi said in a statement.
The area is home to the militant separatist group that's been linked to al Qaeda and known for taking foreigners hostage in recent years.
The tugboat was eventually released, but the whereabouts of the coal-laden barge and 10 crew members are unknown, according to the statement.
Col. Restituto Padilla, a Philippine military spokesman, said authorities were trying to confirm the hijacking.
A military task force was looking into reports from civilians that the barge was taken to Sulu province and may be in the hands of a branch of Abu Sayyaf, the Philippines News Agency reported Tuesday.
"A lot of information is pointing out that the victims were taken to Sulu," Maj. Gen. Demy Tejares, deputy commander of the regional task force, told the agency.
Earlier this month, a video surfaced of foreigners
pleading for their countries to pay ransom to Abu Sayyaf to secure their release.
Two men speaking on the video said they were hostages and Canadian citizens. One said he was "being held by Abu Sayyaf for ransom," although he didn't know how much.
The Canadian government said later that it knew about the video but wouldn't elaborate further.
CNN could not independently verify the authenticity of the video, or the legitimacy of the hostage-takers' claims, including a message from a masked man who urged other countries to "stop procrastinating" and giving them until April 8 to act.
The two purported Canadians were among three male hostages who spoke English on the latest video, which was originally posted to Facebook. Another apparent hostage, a woman, is also visible.