BEIJING (AFP) - Beijing on Friday dismissed an accusation by Manila that the Chinese coastguard robbed Filipino fishermen at gunpoint during a confrontation in the disputed South China Sea, calling the claim "inconsistent with the fact".

The rebuttal came one day after the Philippine fisheries bureau said that fishermen aboard three vessels with clear Chinese coastguard markings boarded two fishing boats in Scarborough Shoal earlier this month and took the crew's catch.

"What we have learned shows that accusations made by the Philippine side are inconsistent with the fact," Chinese foreign ministry spokesman Hong Lei said in a statement posted on the ministry's website.

Using the Chinese name for the disputed area, Hong maintained that Chinese vessels "perform guard duties and keep order in waters off the Huangyan Island in accordance with the law".

He urged Manila to "discipline and educate its fishermen and put an end to its illegal activities".

The Scarborough Shoal lies 220 kilometres off the main Philippine island of Luzon, and is 650 kilometres 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.

In the confrontation earlier this month, 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.

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.

The Philippines has said it will file a diplomatic protest over the incidents.