The vessel was abandoned at a port on Jolo, more than 500 kilometres from the Samal island resort where two Canadians, a Norwegian and a Filipina were abducted late Monday, Brigadier-General Alan Arrojado said.
Jolo is the main base of the Abu Sayyaf, an Al-Qaeda-linked group that has been blamed for the Asian country's deadliest terror attacks, beheadings, and ransom kidnappings of foreign tourists and Christian missionaries.
"We have eyeballed the seacraft, but not the kidnap victims from Samal," Arrojado, head of a Jolo counter-terrorism task force, told reporters.
Officials would not say if the discovery pointed to possible Abu Sayyaf involvement in the kidnapping of Canadian tourists John Ridsdel, 68, and Robert Hall, 50, as well as Norwegian resort manager Kjartan Sekkingstad, 56, and Hall's girlfriend Marites Flor.
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No group has claimed responsibility or demanded ransom for the abductions, the latest in Mindanao, a region plagued by decades of Muslim as well as communist insurgencies, the military said.
Arrojado said the boat suspected of taking the hostages to Jolo was fitted with two onboard engines, but was taking in water apparently from a breach in its hull.
Regional police spokesman Antonio Rivera told AFP that of all the "threat groups" in the south, those based on Jolo were the ones most skilled in using boats.
However, he added: "We cannot say that they (Abu Sayyaf) are involved at this time."
The Abu Sayyaf raided another upscale Samal resort in 2001, killing two people, but were repulsed by the resort's private guards.