The Philippines strongly protested against China Tuesday after Filipino fishermen accused the Chinese coastguard of attacking them with water cannon near a disputed shoal.

The foreign department summoned the Chinese charge d'affaires to receive the formal protest over the January 27 incident at the Scarborough Shoal, said department spokesman Raul Hernandez.

The Chinese foreign ministry dismissed the protest while reiterating Beijing's sovereignty over the area.

"The Chinese vessel continuously blew its horn and thereafter doused the fishing vessels with water cannon for several minutes," Hernandez told reporters.

Fourteen Filipino fishing boats were in the area at the time, and have since safely returned to port in the Philippines without injuries or further incidents, he added.

"The department... strongly protest(s) the efforts of China to prohibit Filipino fishermen from undertaking fishing activities in the Philippines' Bajo de Masinloc," he added, referring to the South China Sea shoal by its Filipino name.

"Bajo de Masinloc is an integral part of the Philippines and over which the Philippines exercises sovereignty, sovereign rights and jurisdiction."

The rocky outcrop lies just 220 kilometres (135 miles) off the main Philippine island of Luzon.

Scarborough is about 650 kilometres from Hainan island, the nearest major Chinese land mass. But Beijing claims most of the South China Sea including waters and outcrops near the shores of its neighbours.

Hernandez said one of three Chinese coastguard vessels in the area fired water cannon at two Filipino fishing vessels which were about 30-40 yards from the shoal.

- 'Respect our sovereignty' -

"The department also received information about nine similar reports of similar harassment incidents of Filipino fishermen" by Chinese vessels since last year, he said.

In these instances, "even during inclement weather conditions Philippine fishing vessels were driven away from the area".

Chinese embassy spokesman Zhang Hua said Beijing rejected the protest, insisting the area is part of Chinese territory.

"The Chinese side does not accept the so-called "protest" by the Philippine side. We urge the Philippine side to work with the Chinese side to resolve differences through bilateral consultations and negotiations," he said in a statement.

In Beijing, foreign ministry spokeswoman Hua Chunying said the Chinese vessel was upholding Chinese sovereignty and maintaining order in waters off Huangyan, the Chinese name for the shoal.

"As for the foreign vessels in these waters the Chinese official vessels deal with that within a very justifiable and reasonable scope," she added.

"We hope that relevant countries will respect China's sovereignty to stop making new trouble."

China and the Philippines engaged in a tense standoff in the area in April 2012, which ended with the Philippines retreating from the shoal.

The South China Sea is home to vital shipping lanes and is believed to sit atop lucrative mineral deposits.

Hernandez said Filipino fishermen had "every right to pursue their livelihood in Bajo de Masinloc", and urged China to "respect our sovereignty".

Asked about measures to be taken to protect Filipino fishermen, military spokesman Lieutenant-Colonel Ramon Zagala told reporters the incident "does not merit a military response".

"We wish to de-escalate the situation there. We are using a rules-based international tribunal arbitration and we are a peace-loving country. Our policy is to avoid confrontation to support...the peaceful solution of the problems we're having in the region."

The foreign department's statement came shortly after President Benigno Aquino acknowledged that security officials were not sure whether using water cannon on Filipino fishermen was a standard operating procedure by the Chinese.

The Philippines, along with Brunei, Malaysia, Taiwan and Vietnam, also have claims to parts of the South China Sea, and the rivalries have been a source of tension for decades.

Last year Manila asked a United Nations arbitration tribunal to rule on the validity of China's claim to most of the sea, but Beijing has rejected the process.