The incident came a month after a Filipino coastguard vessel opened fire on a Taiwanese fishing vessel near an island in the northern Philippines, killing a crew member and sparking a diplomatic row with Taiwan.
Marine rangers saw the small vessel at the remote Tubbataha Reef late Saturday in the Sulu Sea in the far south of the country, and sought the navy's help after a failed chase, park superintendent Angelique Songco said.
"It was dark and they turned off their lights. They had one light on the rear but when they saw our boat coming, they turned it off and ran."
In response to the plea for help, the navy dispatched a patrol gunboat and a surveillance aircraft to the area, but they failed to find or identify the vessel, navy spokesman Lieutenant Stanley Gonzaga told AFP.
Songco said the mystery vessel was flying a Philippine flag but the rangers were convinced that was a ruse. She said one of the rangers, an ex-navy officer, told her its shape was the same as Vietnam's fishing fleet.
Presidential spokesman Edwin Lacierda said the coast guard had been ordered to investigate whether it was a Vietnamese vessel.
The Vietnamese embassy spokesman in Manila could not be reached for comment today.
The 2,30,000-acre Tubbataha Reef is the country's largest marine protected area and was listed as a World Heritage Site by the United Nations in 1993.
A US Navy minesweeper ran aground there in January, damaging a section of the reef and triggering a public outcry.
A Chinese fishing vessel also ran aground on the reef in April, causing even more damage.
It regularly protests the presence of Chinese vessels around Philippine-claimed waters and islands in the South China Sea.
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