Three Philippine troops were injured in the latest China Coast Guard water cannon attack on a Filipino supply vessel near a South China Sea reef, Manila's national security adviser said Sunday.

The Philippine government said Saturday's confrontation caused severe damage to the Unaizah May 4 vessel while it was on its way to deliver troops and provisions to a Philippine navy ship grounded atop the Second Thomas Shoal.

China claims almost the entire South China Sea, brushing off rival claims from other countries, including the Philippines, and an international ruling that its assertion has no legal basis.

National Security Adviser Eduardo Ano said three navy personnel aboard the vessel were injured in Saturday's incident.

The extent and nature of their injuries were not disclosed, though the military said the personnel were treated aboard a coast guard escort ship.

Four crew members were injured by broken glass in an earlier China Coast Guard water cannon attack on the same vessel on March 5.

"This is just an ordinary rotation and resupply or provision operation but look at how the Chinese are reacting," Ano told reporters, according to an interview transcript shared with AFP.

The United States, which has a mutual defence pact with Manila, has denounced the attack.

"The (Chinese) actions are destabilising to the region and show clear disregard for international law," State Department spokesman Matthew Miller said in a statement, reaffirming Washington's mutual defence treaty commitments to Manila.

The China Coast Guard has defended its actions, describing them as "lawful regulation, interception and expulsion" of a foreign vessel that "tried to forcefully intrude" into Chinese waters.

Ano said the damaged vessel has returned to the western province of Palawan after its crew managed to restart its engine. 

"We will not be deterred. We will not be intimidated," he said, vowing the Philippines would continue to resupply the garrison on Second Thomas Shoal.