MANILA — President Rodrigo Duterte on Tuesday said a swarm of Chinese boats in the West Philippine Sea "will not be an obstacle" to Beijing and Manila's COVID-19 vaccine cooperation, despite days of strong rebukes of the incursion by his aides.

At least 3 Cabinet secretaries have expressed frustration over hundreds of Chinese vessels inside the Philippine exclusive economic zone, believed to be manned by militias, which also drew concern from Manila's ally the United States, among others.

The Philippines and China will continue to resolve the issue "through diplomatic channels and through peaceful means," Duterte said in a statement read by his spokesman Harry Roque in a press briefing.

"Whatever differences we have with China will not define our bilateral relations," read the President's statement.

"It will not be an obstacle to the overall positive trajectory of our bilateral friendly relations and our deepening cooperation on pandemic response, including vaccine cooperation and in post pandemic economic recovery."

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The Philippines has one of Asia's worst COVID-19 outbreaks but has faced difficulties securing vaccine supplies.

Two million COVID-19 shots from Beijing-based Sinovac Biotech form the bulk of the Philippines' vaccine inventory so far, half of which were donated by China.

Carlito Galvez Jr, a former military chief leading the Philippine vaccination drive, said the maritime dispute was a "separate" issue from the COVID-19 shots.

Beijing refuses to recognize the 2016 ruling by a United Nations-backed court that invalidated its claims in the South China, including the Philippines' exclusive economic zone, the West Philippine Sea.

China maintained that Julian Felipe Reef was a traditional fishing ground where its vessels were seeking shelter from adverse weather. The reef, which lies within the West Philippine Sea, has seen fair weather but the Chinese ships have remained, Defense Secretary Delfin Lorenzana earlier pointed out, saying he was "no fool" to believe the claim.

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Duterte's statement comes a day after the foreign affairs department said it would protest daily if China refused to withdraw boats that "blatantly infringe" on Philippine sovereign rights. Duterte's legal counsel Salvador Panelo warned of "unwanted hostilities."

• Philippines turns up heat on China over boats massing in South China Sea

Defying public opinion, Duterte has sought to build an alliance with China and has been reluctant to confront its leadership having been promised billions of dollars of loans and investments, much of which have yet to materialize.

He has repeatedly said the Philippines was powerless to stop China from occupying features and that challenging its activities could risk a war his country would lose.

• Tough on US, soft on China? Palace says Duterte being good neighbor to Beijing

— With a report from Reuters