The head of the Philippine armed forces visited a coral-fringed island his country occupies in the South China Sea this week, a move that could stoke already heightened tensions between Manila and Beijing in disputed waters claimed by both countries.

During Monday's visit, Armed Forces of the Philippines (AFP) chief Cirilito Sobejana commended the soldiers for the role they played in protecting the island's residents and "guarding the country's territories" in the strategic waterway.

The visit comes after recent diplomatic protests made by the Philippines over what it says is the illegal presence of hundreds of "Chinese maritime militia" vessels inside its exclusive economic zone and near its occupied islands.

Chinese diplomats have said the boats were just sheltering from rough seas and no militia were aboard.

Sobejana's trip to Thitu, known to Filipinos as Pagasa, happened on Monday, but information was only made public by the AFP on Wednesday.

Thitu is the biggest of the nine reefs, shoals and islands the Philippines occupies in the Spratly archipelago, and is home to a small number of military personnel and civilians.

"(The troops) are in very high spirit, their level of moral is high especially after our visit," Sobejana told reporters on Tuesday evening, adding he also wanted to inspect the island to oversee plans to convert it into a logistics hub to make it easier for naval assets conducting patrols to refuel.

The Chinese Embassy in Manila did not immediately respond to a request for comment.

The Philippines, Brunei, China, Malaysia, Taiwan and Vietnam have competing claims of sovereignty in the South China Sea, a conduit for goods in excess of $3 trillion every year.

The foreign ministers of Southeast Asia and China agreed during a meeting on Monday to exercise restraint in the South China Sea and avoid actions that could escalate tensions.