It was not immediately clear how far the flares that Filipino officials said were fired from the Chinese-occupied Subi Reef were from the Cessna Grand Caravan aircraft of the Philippine fisheries bureau.
Chinese officials did not immediately comment on the incident.
China has claimed virtually the entire South China Sea, a key global trade route, and has vowed to staunchly defend its sovereignty.
Chinese forces have fired flares from its occupied islands and from its aircraft as a warning for foreign planes to move away from what it calls its airspace in the disputed waters.
"The Bureau of Fisheries and Aquatic Resources aircraft recorded video footage of three flares fired from the reef toward the aircraft during its lawful overflight," said the Philippine coast guard, which carried out Saturday's surveillance flight with the fisheries agency.
"These flights aim to monitor the marine environment, assess the status of fisheries resources and ensure the safety and welfare of Filipino fishermen in the West Philippine Sea," the coast guard said, using the Philippine name for the stretch of the South China Sea that the country claims.
The Philippine patrol plane spotted a Chinese hospital ship, two Chinese coast guard ships and 29 suspected militia ships anchored in the waters off Subi, the Philippine coast guard said.
Subi is one of seven disputed and mostly submerged reefs which China turned more than a decade ago into what are now island bases in the Spratlys, the most hotly disputed region of the South China Sea.
The artificial islands are protected by a missile system and three of them have military-grade runways, according to US and Philippine security officials.
Aside from Subi, the Philippine patrol plane flew near six other disputed islands, reefs and atolls, including Sabina, an uninhabited disputed shoal, where it monitored a Chinese navy ship.
"This vessel repeatedly issued radio challenges against the Bureau of Fisheries and Aquatic Resources aircraft while it was flying well within Philippine sovereign rights," the Philippine coast guard said.
"All safe and mission accomplished," Jay Tarriela of the Philippine coast guard said of Saturday's surveillance flight.
Vietnam, Malaysia, Brunei and Taiwan have also been involved in the long-seething disputes in the resource-rich waters.
