China has sought to expand its presence in the disputed waterway for years, brushing aside an international ruling that its claim to most of the sea has no legal basis.

In recent months, Beijing has deployed navy, coast guard and so-called maritime militia forces -- allegedly Chinese fishing vessels -- in a bid to bar the Philippines from strategically important reefs and islands in the South China Sea.

Two such islands -- Philippine-held Thitu and Loaita in the Spratly archipelago -- became the focus of Manila's war games earlier Wednesday as troops executed a manoeuvre to retake the tiny islands from a mock enemy.

A patrol ship and a fast-attack interdictor boat also took part in Wednesday's exercise, with a similar manoeuvre planned later in a Philippine island between the Philippines and Taiwan, exercise director Major-General Marvin Licudine told AFP.

"We will be having island seizure exercises, amphibious counter-landing exercises and air defence exercises," Colonel Michael Logico, an exercise organiser, told reporters Monday at the start of the 12-day war games involving 3,000 navy, army, and air force troops.

"We need to have a persistent presence in the West Philippine Sea," Rear Admiral Roy Vincent Trinidad told a security conference in Manila on Wednesday, adding outlying areas of the Philippine archipelago need to be connected to the "entire country".

Trinidad, the navy's spokesman for South China Sea issues, said that all Filipinos must "understand the existential threat", stressing the process could take years.

In the meantime, "we are capitalising (on) like-minded navies, like-minded nations, our partners and allies and friends", he said, naming Australia, New Zealand, Japan, Vietnam, Canada, the US, Britain, and France.

Elaborating on his speech, Trinidad later told reporters that joint patrols, dubbed Multilateral Maritime Cooperative Activity (MMCA), have reined in Chinese conduct at sea.

"During the conduct of MMCAs, there have been no observed coercive and aggressive actions by the (People's Liberation Army) Navy, Coast Guard or the maritime militia," he said.

The lull was observed for "a few days before and during, and a few days after" the exercises, he said.

Violent encounters with Chinese vessels typically occur during Philippine resupply missions to its remote garrisons in the area.

In Beijing, foreign ministry spokeswoman Mao Ning stressed "China has sovereignty over the South China Sea islands and their adjacent waters" and "we safeguard our sovereign rights and interests in accordance with domestic and international law".

She added: "Making a show of force and provoking confrontation in the South China Sea will only escalate tensions and undermine regional stability."

While Washington and its allies have avoided taking sides in the territorial dispute, they say Chinese actions threaten freedom of navigation essential for trade, with trillions of dollars passing through the waterway each year.