A sister vessel found the unmanned FB Ramona 2 in the Celebes Sea early Tuesday, two hours after the crew of both vessels made their last radio contact, regional military spokesman Major Filemon Tan said.
Tan told reporters that seamen from the sister ship "found all crews on board missing and the VHF Radio/GPS was stolen".
He said the Filipino boat captain and three other crew members were believed to have been abducted. The area is close to the remote Sulu island group more than 1,000 kilometres south of Manila.
Tan could not immediately say if the Abu Sayyaf was involved in the latest incident.
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Security forces have been ordered to intercept the kidnappers if they try to land in the Sulu group, he added.
The unmanned vessel was part of a tuna fishing fleet based in the southern Philippines. Tan said the crew were also from the area.
Last week military sources said the Abu Sayyaf still has about 18 foreign hostages and five local captives, many of them seized from vessels off the southern Philippines.