The Philippines alleged Saturday that China had again increased its presence around a disputed shoal and had harassed a Filipino civilian vessel, after the week-old standoff appeared to have eased.

Hours after reporting that all but one Chinese vessel had left the waters off Scarborough Shoal in the South China Sea by Friday, Philippine Foreign Secretary Albert del Rosario said one of the larger vessels later returned.

This boosted the Chinese presence to two vessels, while a Chinese aircraft also arrived and made fly-bys above a Philippine coast guard vessel stationed in the area, he said.

A Chinese ship also harassed a Philippine-registered vessel conducting a scientific survey, del Rosario said without elaborating.

"It appears that there is an element that is lacking in our negotiations," he said in a written statement to reporters after receiving an updated report from the coast guard.

The crisis started Sunday when the Philippines found 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 despatched three civilian vessels to take turns blocking the Philippine ship.

Talks between del Rosario and the Chinese ambassador to Manila, Ma Keqing, to resolve the dispute went nowhere according to the Philippine side.

However, earlier Saturday del Rosario said all eight fishing vessels as well as two of the three larger Chinese vessels blockading the Philippine forces had fled the area, leaving one vessel left for each of the two claimants.

The Filipino official did not specify whether the alleged fresh Chinese reinforcements had arrived Friday or Saturday.

Del Rosario said the civilian Filipino vessel that was harassed was conducting an "archaeological survey" and that the people on board included nine French citizens.

However he did not specify where the alleged harassment occurred.

Foreign department spokesman Raul Hernandez did not immediately answer queries sent by AFP regarding the Filipino civilian vessel.

The military has said a Philippine coast guard vessel remains near the shoal, about 230 kilometres (140 miles) west of the country's main island of Luzon, monitoring the Chinese activity.

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.

However 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 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.