The research vessel Xiang Yang Hong 33, which is capable of supporting submersible craft, was operating near a reef in the contested Spratly Islands chain, the Philippine Coast Guard said.

The Chinese ship was deploying a service boat towards the Spratlys' Iroquois Reef on Wednesday when it was spotted by a Coast Guard plane, "confirming ongoing unauthorized (marine scientific research) operations", it said in a statement.

Iroquois Reef is located at the southern end of Reed Bank, an area in the Spratlys thought to be rich in natural gas and oil.

During the flight, Manila's Coast Guard also spotted 41 "maritime militia vessels" anchored in waters surrounding Iroquois Reef and Philippine-occupied Thitu Island, home to about 400 Filipinos and a new coast guard station.

"The Philippines has not granted such consent to the (People's Republic of China) for any (marine scientific research) activities in these waters," the Coast Guard said.

"The presence of the research vessel and the large-scale swarming by Chinese Maritime Militia vessels represent a serious infringement on Philippine sovereign rights and maritime jurisdiction."

Beijing's embassy in Manila pointed to its "historic rights" and said in reply that the relevant islands and reefs in question were Chinese territory.

It said China's scientific research vessels conducted each of their missions in accordance with international law.

The Xiang Yang Hong 33, which left China more than three weeks ago, has been monitored conducting surveys near various Philippine-claimed features in the Spratlys, including the flashpoint Sabina Shoal and Second Thomas Shoal.

Beijing claims almost the entire South China Sea, despite an international ruling that its assertion has no legal basis, and defends its actions against Philippine vessels as lawful and proportional.

It has been deploying navy, coast guard and maritime militia forces -- allegedly Chinese fishing vessels -- in a bid to bar the Philippines from strategically important reefs and islands in the disputed waterway.