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.
He urged Manila to "discipline and educate its fishermen and put an end to its illegal activities".
The Scarborough Shoal lies 220 kilometres (about 140 miles) off the main Philippine island of Luzon, and is 650 kilometres (408 miles) from Hainan island, the nearest major Chinese land mass.
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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.
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.