More than 200 Chinese boats were first spotted on March 7 at Whitsun Reef, around 320 kilometres (175 nautical miles) west of Palawan Island in the contested South China Sea.

Most of them have since scattered across the Spratly Islands, but last week dozens of the Chinese-flagged vessels were still anchored at the boomerang-shaped reef, according to Philippine military patrols.

For weeks Manila has called on Beijing to withdraw the "maritime militia" vessels, saying their incursion into the Philippines' exclusive economic zone is unlawful.

But China -- which claims almost the entirety of the resource-rich sea -- has refused, insisting they are fishing boats sheltering from bad weather and are allowed to be there.

Duterte, who has fostered warmer ties with his superpower neighbour since taking office in 2016, has expressed concern to the Chinese ambassador over the ships, according to his spokesman.

Until Monday he had left the tough talking in public to his defence and foreign ministers.

But in the strongest remarks yet from his office, Duterte's top legal counsel Salvador Panelo warned China's "present territorial incursions is producing an unwelcome stain in their bond and may trigger unwanted hostilities that both countries would rather not pursue."

"The matter of territorial dispute has to be resolved in the diplomatic negotiating table or by the dictates of international law," Panelo said in a statement.

It comes a day after outspoken Defence Secretary Delfin Lorenzana accused Beijing of planning to occupy more "features" in the waters -- where Taiwan, Vietnam, Malaysia and Brunei also have rival claims.

Beijing often invokes the so-called nine-dash line to justify its apparent historic rights over most of the South China Sea, and has ignored a 2016 international tribunal decision that declared this assertion as without basis.

The Philippine foreign ministry, which has already lodged a diplomatic protest over the ships, vowed Monday to send a complaint "for every day" Beijing delays pulling out the vessels.

In an apparent reference to China's donation of Covid-19 vaccines, Panelo said the Philippines appreciated the "humanitarian gesture".

But he added: "We will not be blinded however by any act done by it in violation of international law and in derogation of our sovereign rights."