The presence of the vessels in the area could also set back regional cooperation, Manila said in a diplomatic note sent to the Chinese embassy on Wednesday, acting Foreign Secretary Tomas Padilla said. It violated a code of conduct between the two countries requiring them not to take action that would disturb peace in the area, the note said.
"In order not to harm relations and set back the cooperation slowly developing in the region, the Philippine government therefore calls on the Chinese government to withdraw the three Chinese naval vessels from the vicinity of Kalayaan and Panata islands." Padilla told reporters.
President Fidel Ramos ordered the filing of the protest after air force planes reported sighting the three armed ships, accompanied by fishing boats, near two of the eight islands occupied by Philippine troops.
The Spratlys are a cluster of isles, reefs and shoals in the South China Sea believed to be rich in oil and gas. Peking says the area historically belongs to China. The islands are also claimed wholly or in part by Vietnam, Taiwan, the Philippines, Malaysia and Brunei.
Tension flared between the Philippines and China in 1995 when Manila accused the Chinese of building what it said appeared to be naval support structures on Mischief Reef. Peking said they were fishermens' shelters.
In addition to the three naval ships, air force planes saw several fishing boats, including a cargo-type vessel with a landing deck for helicopters, de Villa told reporters. "We are saying that they are inside our Kalayaan municipality and that there is no prior notice, and that there has been no advice that they will be there," de Villa said.