Chinese foreign ministry spokesman Guo Jiakin said the accusation was “completely unbelievable and not even worth refuting”.
“The Philippines has illegally harassed Chinese fishing vessels engaged in normal fishing activities,” he added.
The Philippine National Security Council (NSC) said the alleged poisoning began last year around Second Thomas Shoal, part of the Spratly archipelago in the South China Sea.
The reef is home to a small Philippine military outpost aboard the BRP Sierra Madre, a rusting World War Two-era ship deliberately grounded there in 1999 to assert Manila’s claim to the territory.
NSC assistant director-general Cornelio Valencia said the use of cyanide was intended to “kill local fish populations, depriving Navy personnel of a vital food source”.
He told a press conference on Monday that it also posed health risks to troops by contaminating the water and fish, and could damage the coral reefs that help support the vessel’s structural foundations.
Valencia added that Manila had raised the alleged poisoning with Beijing at a recent meeting but had received no formal response. The NSC intends to submit a report to the foreign ministry that could form the basis of a diplomatic protest.
The navy and coastguard have been ordered to increase patrols in the area.