The vessel was abandoned at a port on Jolo, more than 500 kilometres (311 miles) 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.
"They (local police) are sending us a picture for validation," Arrojado later told AFP a day after the authorities found the 25-metre (82-foot) outrigger at a port in the Jolo town of Parang on Friday.
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.
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.
The Filipina hostage's relatives declined to speak to an AFP photographer who visited them Saturday at their home in the southern town of Quezon.
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.
The authorities earlier said they had received reports the kidnappers had taken their victims to an impoverished region to the east of Samal.
However Rivera told AFP Saturday "no boat was seen there contrary to what was earlier reported".
Jolo-based Abu Sayyaf and several other renegade Muslim rebel groups have in recent years worked together to kidnap foreigners elsewhere in the south, with the victims eventually taken to back Jolo, security analyst Rodolfo Mendoza told AFP.
"They have done it not only on western Mindanao (including Jolo) but they are now also doing it on the eastern Mindanao side," said Mendoza, president of the Manila think-tank Philippine Institute for Peace, Violence and Terrorism.
He cited the case of Australian man Warren Rodwell, held hostage by the Abu Sayyaf for 15 months until released in early 2013, after being seized from his home elsewhere in the Mindanao region.
"They are targeting foreigners because they know that they can collect tremendous sums from them," Mendoza said of Mindanao kidnappings in general.
He said it was well known in the region that Ridsdel, one of the Canadian hostages, had previously worked in Mindanao as president of a gold mining firm operated by TVI Pacific.
The Abu Sayyaf is currently holding four other foreigners -- a Dutch man, a South Korean and two Malaysians, according to the military.