The sailors were abducted nine months ago in Malaysian waters and taken to the remote southern Philippine island of Jolo, a stronghold of the suspects from the Abu Sayyaf group, Islamist militants engaged mainly in kidnappings for ransom.
Their ordeal ended when they turned up at a military checkpoint on Jolo shortly after Philippine troops clashed with their suspected kidnappers in a nearby town, the local military chief said.
"Our soldiers spotted them at a checkpoint where they were on board a public utility vehicle," Brigadier General Cirilito Sobejana, task force commander for the region, told AFP.
Five Abu Sayyaf members were killed and five soldiers were wounded in that firefight, he added.
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The two were abducted in November off the Malaysian state of Sabah that had for years suffered from repeated kidnappings by the Abu Sayyaf.
The kidnappers still hold 15 other hostages, all but two of them foreigners, the general said.
One Vietnamese sailor was rescued last month after nine months in captivity.
Elderly German yachtsman Jurgen Kantner, was beheaded in February after the kidnappers' demand for USD 600,000 was not met.
The kidnappers had also murdered his woman partner and compatriot during his kidnapping at sea four months earlier.
Last year, the group beheaded two Canadian hostages.
Abu Sayyaf, originally a loose network of militants formed in the 1990s with seed money from Osama bin Laden's Al-Qaeda network, has splintered into factions, with some continuing to engage in banditry and kidnappings.
The militants continue to occupy parts of the southern city despite a US-backed military offensive there that has claimed nearly 800 lives and displaced nearly 400,000 people.
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