The Philippines accused the Chinese coastguard on Thursday of robbing Filipino fishermen at gunpoint during a series of confrontations at a disputed shoal in the hotly contested South China Sea.

Fishermen aboard three vessels with clear Chinese coastguard markings boarded two Philippine fishing boats in Scarborough Shoal on April 11, then took the crew's catch, the Philippine fisheries bureau said.

In one incident, the Filipino fishermen "were threatened and pointed with a gun before the Chinese forcibly took their fishes," according to an incident report from the bureau sent to AFP.

The gunmen also destroyed the Filipinos' fishing equipment, the report said.

The two boats were among 20 Filipino vessels on an expedition in Scarborough Shoal, a rich fishing ground within the Philippines' exclusive economic zone, it said.

A week later three Chinese coastguard ships fired water cannon on a Philippine fishing boat, injuring at least three crewmen and destroying the ship's glass windows, according to a separate report from the bureau.

"This is unacceptable because the area is within our exclusive economic zone," Philippine fisheries bureau head Asis Perez told AFP.

"No country has the right to stop our fishermen from doing their jobs. That's against international law."

Asked about the incidents on Thursday, Philippine foreign affairs spokesman Charles Jose said the government would file a diplomatic protest.

The Scarborough Shoal lies 220 kilometres (about 140 miles) off the main Philippine island of Luzon, and is 650 kilometres (408 miles) from Hainan island, the nearest major Chinese land mass.

China took control of the shoal following a tense standoff between Chinese maritime patrol vessels and the Philippine navy in 2012.

Armed Chinese coastguard vessels have patrolled the shoal since then, restricting access for Philippine fishing boats, Manila has said.

Chinese foreign ministry spokesman Hong Lei said Wednesday Filipino fishermen had "no permission" from the Chinese government to be in the shoal.

"The Chinese side calls on the Philippine side to show earnest respect for China's territorial sovereignty, step up its regulation and education of the fishermen and stop all actions infringing upon China's territorial sovereignty, and rights and interests," he said.

China claims nearly all of the South China Sea, even waters and islands close to the coast of the Philippines and other Asian neighbours.

Renewed tension over the Scarborough Shoal has come amid alarm in the Philippines and the United States over giant Chinese reclamation on seven contested reefs in the Spratlys archipelago --also in the South China Sea.

Vietnam, Malaysia, Brunei and Taiwan also have overlapping claims in the sea, which hosts vital shipping lanes and is believed to contain vast mineral reserves.

Earlier this week, close to 12,000 Filipino and American soldiers kicked off expanded war drills, including an amphibious assault exercise, at a navy base facing Scarborough Shoal.

The exercise simulated re-taking a Philippine island occupied by invaders.

An editorial by the Beijing-based Global Times ridiculed the US-Philippines alliance, calling Manila a "cute little submissive" to Washington.

But Jose parried the attack, saying: "Unable to defend their unlawful position (in the disputes), our northern neighbour has reduced its lack of a response to name-calling."