China has protested about a visit by Philippine military chiefs to a disputed island in the South China Sea, but Manila maintained on Saturday that it owns the territory where Filipino troops and villagers have lived for decades.

The public argument comes amid a thaw in once-frosty relations between the neighbours after Philippine President Rodrigo Duterte took office last June and moved to rekindle Manila's friendship with Beijing, which has been strained by long-seething territorial disputes.

Philippine Defence Secretary Delfin Lorenzana and military Chief of Staff General Eduardo Ano flew to the island, which Filipinos call Pag-asa, with dozens of journalists on Friday to inspect an eroded airstrip.

The Philippine government plans to reinforce and lengthen the facility and build a dock starting next month to accommodate ships with construction materials, Lorenzana said.

OPINION: Why China cares about the South China Sea

About $32m has been earmarked for the construction, including a fish port, solar power, water desalination plant, improved housing for soldiers and facilities for marine research and tourists.

Accompanied by military top brass, Lorenzana and Ano also met Filipino troops and villagers and took part in a flag-raising ceremony on Pag-asa, which is internationally known as Thitu and is called Zhongye Dao by China. It's the second-largest island in the South China Sea's hotly contested Spratlys archipelago.

In Beijing, Foreign Ministry spokesman Lu Kang expressed China's displeasure over the high-profile Philippine visits to the island, saying Beijing was "gravely concerned about and dissatisfied" by the island visits, adding that it "has lodged representations with the Philippine side".

"We hope that the Philippine side could cherish the hard-won sound momentum of development the bilateral relations are experiencing, faithfully follow the consensus reached between the two leaderships, maintain general peace and stability in the South China Sea," Lu said.

The Philippine government replied by saying that the island was part of an island municipality under its western province of Palawan, which faces the disputed waters.

"Our visits there are part of the government mandate to ensure the safety, wellbeing, livelihood and personal security of our citizens there," Department of Foreign Affairs spokesman Robespierre Bolivar said in a statement.

During the trip to Pag-asa, Chinese forces tried to drive away two Philippine air force planes that carried Lorenzana, Ano and others as they flew near a Chinese man-made island called Subi, just 25km away.

South China Sea: Weapons systems installed on islands

Lorenzana said that their aircraft continued uninterrupted without any incident after Filipino pilots messaged back to the Chinese that they were flying over Philippine territory. The Chinese warned the Philippine aircraft that they were entering the periphery of Chinese installations and told to avoid miscalculation.

The Chinese navy has similarly warned US ships and aircraft to leave what Beijing claims as its territory, messages the Americans also ignored.

China claims virtually the entire sea and has aggressively tried to fortify its foothold by transforming in recent years seven mostly submerged reefs into island outposts, including Subi.

Three of the artificial islands were built with runways, along with buildings, towers, radars and more recently weapons systems, to the consternation of other Asian claimant governments and the United States, which insists on freedom of navigation in international waters.