Talks between the Philippines and China over boats in a disputed shoal, remained in a "stalemate" despite the departure of all but one Chinese vessel from the area, the foreign secretary said Saturday.

Philippine Foreign Secretary Albert del Rosario also confirmed the eight Chinese fishing vessels that sparked this maritime standoff had fled the disputed Scarborough Shoal even while the talks were going on.

Del Rosario said in a statement that he only learned of the departure of the Chinese boats while negotiating late Friday with Chinese ambassador Ma Keqing on the dispute.

"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 military has said a Philippine coast guard vessel remains at Scarborough Shoal, about 230 kilometres (140 miles) west of the country's main island of Luzon, monitoring a Chinese marine vessel.

The Chinese vessel is one of three Chinese civilian ships that took turns preventing the Philippines from arresting the Chinese fishermen after they were caught fishing in Scarborough Shoal on Sunday.

Del Rosario also said it was "regrettable" the fishing boats were allowed to leave without the Philippines confiscating their catch of endangered species like giant clams, corals and live sharks.

The head of Philippine military forces in the area, Lieutenant General Anthony Alcantara said tension in the area had been "defused," by the departure of most of the Chinese boats.

But he stressed the coast guard ship would stay in the area.

The crisis started 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.

A Philippine coast guard ship later replaced the navy ship but on Friday, it was reported that three of the eight Chinese fishing boats had left the shoal. A day later, all eight were found to have fled.

The Philippines says the shoal is in its territory, well within the country's 200-nautical-mile exclusive economic zone, as recognised by international law.

However China has insisted the shoal is Chinese territory as part of its claim to all of the South China Sea, even waters up to the coasts of other countries.

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 standoff is the highest-profile in recent years.

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