General Emmanuel Bautista said Chinese vessels fired cannon on January 27 near Scarborough Shoal - the subject of a bitter territorial row in the strategically important South China Sea.
"The Chinese coast guard tried to drive away Filipino fishing vessels to the extent of using water cannon," Bautista told a forum of the Foreign Correspondents Association of the Philippines.
He did not say if anyone was hurt and added that China continues to maintain an armed coast guard and other vessels at the shoal.
Scarborough Shoal lies 220 kilometres off the main Philippine island of Luzon. It is about 650 kilometres from Hainan island, the nearest major Chinese land mass.
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In April 2012, the Philippines and China had a tense standoff which ended with the former retreating from the shoal- a rich fishing area.
China has occupied the shoal as part of its claim to most of the South China Sea including waters near the coasts of its neighbours.
The Philippines, along with Brunei, Malaysia, Taiwan and Vietnam also have competing claims to parts of the 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 refused to be part of the process.
"We continue to give primacy to its (the dispute's) peaceful resolution principally through international arbitration," Bautista said.
"All our actions are in support to that. We remain hopeful that the issue can be resolved peacefully and result in peace and stability in the region."
"We will continue to perform that mandate with whatever we've got," he said, adding that the country was in the first phase of modernising its poorly-equipped armed forces.