The Philippine military on Saturday accused China's air force of "dangerous and provocative actions" against a military plane patrolling over a disputed South China Sea reef.

Two China air force aircraft "executed a dangerous manoeuvre at around 9:00am and dropped flares in the path of our NC-212i," armed forces chief General Romeo Brawner said in a statement, recounting the alleged incident Thursday "over" Scarborough Shoal.

He said the Chinese action "endangered the lives of our personnel undertaking maritime security operations," adding that the pilot and crew "safely returned" to a northern Philippines air base.

The allegation was the latest in an increasingly tense confrontation between Manila and Beijing, which claims most of the South China Sea and seized the shoal after a 2012 standoff with the Philippines.

In an earlier clash the Philippine military said one of its sailors lost a thumb in a confrontation off Second Thomas Shoal in another area of the South China Sea in June in which the Chinese coastguard also confiscated or destroyed Philippine equipment including guns.

The Chinese air force action supposedly took place a day after China carried out a combat patrol near the flashpoint reef to test the "strike capabilities" of its troops.

Beijing claims almost the entire South China Sea, brushing off rival claims of several Southeast Asian countries, including the Philippines, and an international ruling that its assertion has no legal basis.

Scarborough Shoal, a triangular chain of reefs and rocks, is 240 kilometres (150 miles) west of the Philippines' main island of Luzon and nearly 900 kilometres from the nearest major Chinese land mass of Hainan.

Brawner said the Philippine military "strongly condemns the dangerous and provocative actions of the People's Liberation Army Air Force that endangered the lives of our personnel undertaking maritime security operations recently within Philippine maritime zones".

"The incident posed a threat to Philippine Air Force aircraft and its crew, interfered with lawful flight operations in airspace within Philippine sovereignty and jurisdiction, and contravened international law and regulations governing safety of aviation," he added.

A Philippine military spokesman told AFP the Chinese aircraft involved in the incident were "MRF", an abbreviation for multi-role fighter jets.