China and the Philippines have engaged in months of confrontations in the contested South China Sea, which Beijing claims almost entirely, despite an international ruling that the assertion has no legal basis.

Wednesday's encounter happened near a group of small sandbanks in the Spratly Islands where two Filipino ships were collecting sand samples "as part of a marine scientific research initiative", the Bureau of Fisheries and Aquatic Resources said in a statement.

"At approximately 0913H, CCG vessel 21559 water cannoned and sideswiped the BRP Datu Sanday (MMOV 3002) twice ... putting at risk lives of its civilian personnel."

It was the first time water cannon were used against Philippine vessels near the disputed Sandy Cay reef, the bureau added.

The "aggressive interference, dangerous manuevers, and illegal acts" damaged the Philippine ship's port bow and smokestack, according to the bureau's statement.

The Philippines scientific team was still able "to complete its operations in Pag-Asa Cays 1, 2 and 3", the statement said, using the Philippine term for the Sandy Cays.

China's foreign ministry spokeswoman Mao Ning said she was not aware of the incident. "What I can tell you is that the Chinese Coast Guard always enforces the law in accordance with laws and regulations," she said.

Last month, the Philippines slammed as "irresponsible" a Chinese state media report claiming that Sandy Cay 2 was put under China's control.

Chinese state broadcaster CCTV said that the country's coast guard had "implemented maritime control" over Tiexian Reef in mid-April.