China claims almost the entirety of the resource-rich sea, and has been accused by the United States of efforts to "intimidate, coerce and threaten other nations" to control it.

The Philippines on Sunday said more than 200 militia boats were spotted "in line formation" at the boomerang-shaped Whitsun Reef around 320 kilometres (175 nautical miles) west of Palawan Island on March 7.

Manila called on China to "immediately recall these boats violating our maritime rights and encroaching into our sovereign territory".

But Beijing disputed the claim, saying that "for a long time, Chinese fishing boats have been fishing in waters near the reef", which it said was a part of the contested Spratly Islands.

"Recently, due to conditions at sea, some Chinese fishing boats have been sheltering from the wind near the Whitsun Reef," foreign ministry spokeswoman Hua Chunying told reporters.

"We believe this is very normal, and hope all parties can consider it rationally."

The Philippines' Foreign Secretary Teodoro Locsin said on Twitter he had lodged a diplomatic protest over the vessels.

An aerial patrol of the reef on Monday detected "around 183" vessels, the Armed Forces of the Philippines chief Lieutenant General Cirilito Sobejana said in a statement.

Beijing often invokes the so-called nine-dash line to justify its apparent historic rights over most of the South China Sea, parts of which are also claimed by Taiwan, Malaysia, the Philippines and Brunei.

China has ignored a 2016 international tribunal decision that declared its assertion as without basis.