Two Vietnamese fishermen were found dead with gunshot wounds and five others were arrested after the Philippine navy chased suspected poachers in the South China Sea at the weekend, authorities said Monday.

A Philippine patrol ship pursued six Vietnamese fishing boats 56 kilometres (30 nautical miles) off the northern coastal town of Bolinao before dawn Saturday, a regional military spokesman told AFP.

The bodies of the two men were found after a Vietnamese boat slammed into the Philippine vessel, said Lieutenant Jose Covarrubias.

The five fishermen in custody would face poaching charges as they were within Philippine waters, he added.

"The navy ship spotted the six fishing boats (which were) using bright lights to attract fish. While it was chasing the boats, one boat manoeuvred and hit our vessel," said Covarrubias.

"The officers boarded and searched the boat, resulting in the apprehension of the five and they found the two dead bodies."

The Philippine foreign affairs department said navy personnel had fired warning shots after the Vietnamese vessel had initiated "very dangerous manoeuvres".

Covarrubias said he could not confirm this.

A police report released Monday said it found gunshot wounds on the bodies of the two fishermen while their vessel sustained six bullet holes.

The fishermen's bodies would undergo an autopsy, the report said.

Foreign fishermen have often been caught trespassing in Philippine waters. Last year President Rodrigo Duterte ordered the release of 17 Vietnamese fishermen caught in his nation's waters.

In 2013 the Philippines apologised to Taiwan over the killing of a Taiwanese fisherman by Filipino coastguards who said his vessel had illegally sailed into local waters.

Taiwan suspended the hiring of Philippine workers and recalled its de facto representative to Manila in protest.

Foreign Secretary Alan Peter Cayetano said the Philippines would conduct a "fair and thorough" investigation into the deaths of the Vietnamese, according to a foreign department statement.

"We would like to offer our sympathies over the unfortunate loss of life," Cayetano told Vietnamese Foreign Minister Pham Binh Minh on the sidelines of the United Nations General Assembly in New York.

Vietnam's foreign ministry urged Philippine authorities to "take strict action" if any mistakes by Philippine forces were found.

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