Beijing claims the strategic South China Sea in nearly its entirety, despite an international ruling that its assertion has no legal basis.
The Philippines' National Security Council (NSC) alleged the poisoning began last year around Second Thomas Shoal in the Spratly chain, which sits near vital shipping lanes and is reputedly rich in minerals.
"The use of cyanide on Ayungin Shoal is a term of sabotage that seeks to kill local fish populations, depriving Navy personnel of a vital food source," NSC assistant director-general Cornelio Valencia told a news conference, using the Philippines' term for the reef.
These actions also "threaten our Navy personnel" through exposure to contaminated water, eating poisoned fish, as well as eroding corals, Valencia added.
Manila and Beijing have a long history of maritime territorial disputes in the hotly contested waterway, including a violent clash in June 2024 in which Chinese coastguard personnel wielding knives, sticks and an axe boarded Philippine Navy boats.
China's foreign ministry branded the fresh accusations a "farce".
It is "completely unbelievable and not even worth refuting", spokesman Guo Jiakun told a regular news briefing on Monday.
"The Philippines has illegally harassed Chinese fishing vessels engaged in normal fishing activities, robbing fishing people of their supplies," he added.
- Cyanide bottles -
Valencia said Manila had raised the alleged poisoning with Beijing at a recent meeting but has received no formal reply.
He added that reef damage from cyanide poisoning could also compromise the structural foundations of the BRP Sierra Madre, a World War II-era warship on which the Filipino troops are stationed.
Manila deliberately grounded the vessel on the shoal in 1999 to stake its claim to the territory.
Philippine Navy spokesman Rear Admiral Roy Vincent Trinidad said Filipino troops had seized 10 bottles of cyanide from sampan boats launched from Chinese fishing ships in February, July and October 2025.
He said that soldiers observed another Chinese sampan crew poisoning waters near the shoal last month, adding that the shoal's waters later tested positive for cyanide.
None of the troops aboard the warship have tested positive for the poison, Trinidad added.
Valencia and Trinidad both alleged the fishermen's mother ships worked for the Chinese Navy.
Valencia said the NSC planned to submit a report next week to the Philippine foreign ministry which could become the basis for a diplomatic protest.
Manila has also ordered the navy and coastguard to step up patrols "to prevent further environmental harm" in the area, he added.