China has asked all Philippine vessels immediately to leave Panatag Shoal, as the South China Sea area is called in the Philippines, and sent a second aircraft to harass Filipino fishermen, officials in Manila said.
The aircraft flew past the ships at less than 500 feet, continuing a spat that started earlier this month.
The shoal is a triangular collection of reefs covering less than 60 square miles and whose highest point is around 10 feet above sea level.
The shoal is more than 400 miles off the Chinese coast but 150 miles off the coast of Zambales, a province on the western shore of Luzon Island, the largest and most northern Philippines island.
Philippine Defense Secretary Voltaire Gazmin said Philippine ships won't leave the area, a report by the Philippine Daily Inquirer said.
"As of now we still have a standoff because we are told to leave but we won't leave and we tell them to leave but they don't want to leave," Gazmin said.
"We will fight for what is ours. We are in the area and we will not leave while we continue the talks between our Department of Foreign Affairs and Chinese authorities."
His comments come after the Chinese Embassy in Manila insisted that Panatag, which China calls Huangyan Island, is within China's maritime zone, the Inquirer report said.
"We urge the archaeological vessel to leave the area immediately," spokesman Zhang Hua said in a statement.
"It is China that first discovered this island, gave it the name, incorporated it into its territory and exercised jurisdiction over it," the embassy said.
The Chinese statement said several treaties -- Paris 1898, the Treaty of Washington 1900 and a treaty with Great Britain in 1930 -- that set out Philippines territorial limits never referred to Huangyan Island nor included Scarborough Shoal.
But Raul Hernandez, Filipino department of Foreign Affairs spokesman, said the shoal is part of the coastal town of Masinloc in Zambales.
Hernandez said he would "continue to reach a diplomatic solution to the problem," the Inquirer report said.
Philippines Foreign Secretary Albert del Rosario has called on China to settle the issue at the International Tribunal on the Law of the Sea.
"The whole world knows that China has myriad more ships and aircraft than the Philippines," Rosario said in a statement posted on a government Web site.
"Chinese ships are currently engaging in illegal activities within the Philippine exclusive economic zone," he said.
"However, we hope to demonstrate that international law will be the great equalizer. In pursuing a peaceful settlement of the Scarborough Shoal issue, we fully intend to humbly invite our Chinese friends to join us in the International Tribunal on the Law of the Sea."
In December the Philippine navy said it soon would receive its second decommissioned U.S. Coast Guard ship, the former USCGC Dallas, a Hamilton class cutter. The 378-foot-long, 3,250-ton Dallas was commissioned in 1967 at the Avondale Shipyard in New Orleans.
The Scarborough Shoal standoff is part a continuing and larger maritime territorial dispute in which China is claiming many islands, shoals and rocky outcrops stretching south into the South China Sea.
Among the disputed territories are the Paracel Islands and the Spratly Islands.
Last month several local authorities in Vietnam said they will send six Buddhist monks to occupy refurbished shrines and religious buildings on several islands in the disputed Spratlys.
The temples were last inhabited in 1975 but were recently renovated to assert Vietnamese sovereignty over the Spratly Islands, which are off Vietnam in the South China Sea, a BBC report said.
As well as Vietnam and China, ownership of various Spratly islands and reefs -- some only visible at low tide -- are disputed by Brunei, Taiwan, Malaysia and the Philippines, although Brunei doesn't occupy any of the islands.
The Spratly dispute has erupted into open military confrontation on occasions, such as the brief 1988 Johnson South Reef skirmish between China and Vietnam in which about 70 Vietnamese military personnel were killed.