The statement by Beijing comes after Manila said it refuses to abandon the post and summoned China's ambassador to present a strongly worded diplomatic protest over the Chinese use of water cannons in a confrontation with Philippine vessels over the weekend.
Manila accused Beijing of "excessive and offensive actions" against Philippines vessels.
"China once again urges the Philippine side to immediately remove the warship from Second Thomas Shoal and restore it to its unoccupied state," China's foreign ministry said.
China has communicated to the Philippines on the Second Thomas Shoal issue "many times" through diplomatic channels, but its goodwill and sincerity have been "ignored", it added.
Beijing said its use of water cannons comes as a "warning".
The stand-off took place on Saturday near Second Thomas Shoal, which the Philippines has occupied for decades.
Territorial conflicts in the South China Sea involving China, the Philippines, Vietnam, Malaysia, Taiwan and Brunei have been long standing.
The US, the European Union, Australia and Japan supported the Philippines in this regard and expressed concern over China's actions.
Philippine coastguard and diplomatic officials held a news conference on Monday at which they showed videos and photographs, which they said showed six Chinese coastguard ships and two militia vessels blocking two Philippine navy-chartered civilian boats taking supplies to the Philippine forces at Second Thomas Shoal.
One supply boat was hit with a powerful water cannon by the Chinese coastguard, the Philippine military said.
On Tuesday, the Chinese coastguard showed a video of a water cannon spraying near the smaller Philippine vessel without hitting it.
"We urge China not to escalate matters by water cannons or military-grade lasers, which places Philippines lives at risk, but by sincere negotiations and other diplomatic means," Jonathan Malaya, assistant director general of the Philippines' National Security Council, said.
Tensions have soared between the two countries over the South China Sea under Philippine President Ferdinand Marcos Jr, with Manila pivoting back to the US, which supports Manila in its maritime disputes with China.