A fleet of Chinese ships that sparked a diplomatic row after parking at a reef off the Philippines for weeks are now scattered across the contested Spratly Islands, a government agency said Wednesday, condemning Beijing's "unlawful presence" in the area.

Over two hundred ships were first spotted on March 7 at Whitsun Reef, around 320 kilometres (175 nautical miles) west of Palawan Island in the South China Sea.

Manila ordered Beijing to withdraw the ships, calling their presence an incursion into its sovereign territory.

China -- which claims almost the entirety of the resource-rich sea -- has claimed the vessels are fishing ships sheltering from bad weather.

But Manila insists they are from Beijing's Maritime Militia, frequently accused of conducting covert military operations in the area.

Philippines aerial and sea patrols this week recorded 44 of the Chinese-flagged boats still at the boomerang-shaped reef, said a task force charged with monitoring the disputed waters.

Around 210 vessels were now "swarming" other reefs and islands in the area, it said, expressing "deep concern over the continuing unlawful presence of the Chinese Maritime Militia".

Over two hundred ships were first spotted on March 7 at Whitsun Reef, around 320 kilometres (175 nautical miles) west of Palawan Island in the South China Sea Over two hundred ships were first spotted on March 7 at Whitsun Reef, around 320 kilometres (175 nautical miles) west of Palawan Island in the South China Sea Photo: Satellite image ©2021 Maxar Technologies / Handout

The Philippine military said it could not confirm if 92 vessels spotted at Chigua Reef and 84 at Gaven Reef were part of the original flotilla.

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

It has transformed reefs in the Spratly archipelago into islands, installing military facilities and equipment on them.

One of them is Mischief Reef -- which the Philippines also claims -- where the task force said four Chinese navy vessels were spotted during patrols.

The Philippine military said its aircraft received a radio challenge during a surveillance mission, its spokesman said Wednesday.

Local media onboard the flight over Whitsun Reef this week reported the aircraft was told by the Chinese to leave so as "to avoid any move that may cause misunderstanding."

Several countries, including the United States, have expressed concern at the renewed tension in the region.