Talks between the Philippines and China over a fishing dispute in the South China Sea remain deadlocked despite an apparent end to a standoff between Chinese fishing boats and Philippine naval vessels, according to the Philippine government. 

Albert del Rosario, the Philippine foreign secretary, said eight Chinese fishing vessels that sparked the  incident had left waters near the islands of Scarborough Shoal on Friday as negotiations were continuing.

Del Rosario said in a statement that he only learned of the departure of the Chinese boats while meeting Chinese ambassador Ma Keqing on the dispute. He said the Chinese boats had taken their catches with them, despite Philippine efforts to claim the haul.

"The Chinese fishing vessels had left the lagoon, a development which we had been working towards except for our not being able to confiscate their illegal harvest ... which was regrettable," said Del Rosario in a statement.

"The meeting with Ambassador Ma last night resulted in a stalemate as we had demanded of one another that the other nation's ship be first to leave the area," he added.

The Philippine military said a coast guard vessel remained at Scarborough Shoal, about 230 kilometres west of the country's main island of Luzon, monitoring a Chinese marine vessel which was still stationed in the area.

Live sharks

The Philippines had wanted the fishermen to hand over their hauls of giant clams, corals and live sharks in return for safe passage out of the area, but the ships took their catches with them.

The crisis started on Sunday when the Philippines found the eight Chinese fishing boats in the area, which the Philippines claims as its territory.

A Philippine navy warship was preparing to arrest the Chinese fishermen for poaching but China dispatched the three civilian vessels to take turns blocking the Philippine ship.

China has disputes with several countries in the region including the Philippines over areas of the South China Sea, which is believed to be rich in oil and gas and is crossed by important shipping lanes.

Aside from the Philippines and China, Taiwan, Vietnam, Malaysia and Brunei also claim all or parts of the waters as their own.

The Philippines and Vietnam complained last year of increasingly aggressive acts by China in staking its claim to the South China Sea.

However this week's stand-off is the highest-profile in recent years.