Deputy foreign ministers from China and the Philippines held a phone call on Monday, the countries said, after Manila summoned a Chinese envoy over "aggressive actions" by the China Coast Guard in the contested South China Sea.

"Vice Foreign Minister Chen Xiaodong held a phone call with Philippine deputy foreign secretary (Maria Theresa) Lazaro, and made stern representations on issues including the Philippines' transportation of supplies to the illegally "beached" military ship on Ren'ai Reef," China's foreign ministry said in a statement, using the Chinese name for Second Thomas Shoal in the Spratly Islands.

Manila said Lazaro, the undersecretary for bilateral relations and ASEAN affairs, expressed the Philippines' "strongest protest against the aggressive actions undertaken by the China Coast Guard and Chinese Maritime Militia".

Beijing and Manila have a long history of maritime territorial disputes in the South China Sea and there have been repeated confrontations between their vessels near contested reefs in recent months.

The latest incident took place on Saturday near Second Thomas Shoal in the Spratly Islands during a regular Philippine mission to resupply Filipino troops garrisoned on the BRP Sierra Madre, a grounded navy ship.

The Philippines said the China Coast Guard blocked its supply vessel and damaged it with water cannon, injuring three soldiers.

The China Coast Guard has defended its actions, describing them as "lawful regulation, interception and expulsion" of a foreign vessel that "tried to forcefully intrude" into Chinese waters.

Chen told Lazaro in Monday's tense call that "China-Philippines relations are currently at a crossroads, and the Philippines must act prudently".

"China once more urges the Philippines to honour its commitments, respect the consensus, stop violating rights and provoking trouble at sea, stop any unilateral action that could complicate the situation, and earnestly return to the correct track of appropriately addressing disagreements through negotiation and consultation," Chen said.