Department of Foreign Affairs spokesman Raul Hernandez said a diplomatic protest was handed to Beijing's charged affairs over the January 27 incident at Scarborough Shoal, a rich fishing ground claimed by China and the Philippines.
The shoal came under Chinese control after Philippine vessels backed off from a tense standoff with Chinese ships in the area in 2012.
The Philippines has not deployed its ships to try to take back control of Scarborough but asked an international tribunal last year to declare China's seizure of the shoal and seven other South China Sea reefs illegal.
A Chinese coast guard vessel with bow No. 3063 used its water cannon for several minutes and sounded its horn to drive away two Filipino fishing boats near Scarborough, Hernandez told a news conference, adding it was the first time Chinese authorities had carried out such a hostile act against Filipino fishermen.
Filipino fish trader Macario Forones said Chinese coast guard personnel used waste water laden with oil while blowing the horn and yelling "Go away, go away" at his fishermen. One or two other Philippine fishing boats were hit by the waste water, he said.
"The water smelled of oil and smeared the side of my fishing boat," Forones told The Associated Press by telephone. "But my fishermen did not really leave the area. We've spent so much money to travel there and they basically ignored the Chinese."
President Benigno Aquino III said his government wanted an explanation from Beijing.
Chinese Embassy officials did not immediately react to the Philippine protest.
Hernandez said the Philippine government would take steps to protect its fishermen, but he did not specify how.
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