Philippine President Ferdinand Marcos on Sunday condemned what he called "illegal and reckless" actions by China's air force last week against a Filipino military plane patrolling over a disputed South China Sea reef.

Two Chinese air force aircraft undertook a "dangerous manoeuvre" and dropped flares in the path of a Philippine air force turboprop over Scarborough Shoal on Thursday, according to the Philippine military. 

Manila said the Chinese actions put the lives of its crew in danger, but that the patrol plane returned safely to base.

The Chinese actions were "unjustified, illegal and reckless, especially as the PAF (Philippine Air Force) aircraft was undertaking a routine maritime security operation in Philippine sovereign airspace," Marcos said in a statement.

Marcos "strongly condemns" the incident, the statement said, adding it was "worrying that there could be instability in our airspace".

China defended its operations on Saturday, saying it had "organised naval and air forces to lawfully... (drive) away" the Philippine plane, following "repeated warnings".

"We sternly warn the Philippines to immediately stop its infringement, provocation, distortion and hype," said a statement from the Southern Theater Command of the People's Liberation Army, adding that "China has indisputable sovereignty over Huangyan Island (Scarborough Shoal) and adjacent waters".

The incident is 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 June, 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, when the Chinese coastguard also confiscated or destroyed Philippine equipment including guns.

Beijing has blamed the escalation on Manila and maintains its actions to protect its claims are legal and proportional.

Following the Second Thomas Shoal clash, the two countries agreed on a "provisional arrangement" for resupplying Filipino troops based on a decrepit warship grounded atop the reef, and also to increase the number of communication lines to resolve disputes in the waterway.

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