Park Chulhong, skipper of the South Korea-registered carrier DongBang Giant 2, and Filipino Glenn Alindajao, were brought to the house of the island's governor after they were released by the militants of the Abu Sayyaf group, Major Filemon Tan said.
Members of a Muslim rebel faction cooperating with the government in the south of the predominantly Christian country had helped arrange the release, Tan told reporters.
"They were freed this morning with the help of rebels belonging to the Moro National Liberation Front," Tan said, adding the two were flown out of the island by a presidential adviser on peace efforts.
The cargo vessel was sailing to Australia from South Korea when 10 Abu Sayyaf militants boarded it in October and abducted Park and Alindajao.
Presidential peace adviser Jesus Dureza told reporters the government had not paid a ransom, though some media reported that some sort of payment was believed to have been made.
"You know the policy of the government, we don't pay ransom. But, if there was some form of payment made, the government did not play any role in it," the adviser, Jesus Dureza, told reporters.
The Moro National Liberation Front signed a peace deal with the government in 1996 and promised to help President Rodrigo Duterte free hostages and defeat the small but violent Abu Sayyaf, known for kidnappings, beheadings, bombings and extortion.
The Abu Sayyaf group is still holding two dozen captives on Jolo island, its stronghold where more than 10,000 troops have been deployed to fight the militants.
The captives include people from the Netherlands, Japan, Germany, Indonesia, Malaysia and Vietnam.
The waters between the Philippines and Malaysia has become dangerous for merchant shipping due to rising threat of kidnappings, the International Maritime Bureau said this week.
(Reporting by Manuel Mogato; Editing by Robert Birsel)