The Philippines is to upgrade a navy base facing disputed South China Sea waters to serve the extra ships being acquired to protect its territory, the military said Thursday.

Navy spokesman Lieutenant-Commander Gregory Fabic said the military would build a 500-million-peso ($11.2 million) port at Ulugan Bay, the Philippine military base nearest to the Spratly Islands.

"It is being programmed for capability upgrade... we need to develop it to house the big vessels of the navy," he told reporters.

President Benigno Aquino is set to visit the base on May 20 to launch the upgrading, Fabic added.

The base on the west coast of Palawan island is the headquarters of naval forces guarding the waters on the west of the archipelago.

In recent years, the Philippines has been locked in an increasingly tense standoff with China involving disputed reefs and islands in the Spratlys and other areas of the South China Sea.

Under a programme designed to improve the capability of one of Asia's weakest military forces, the Philippines has been acquiring naval vessels to create what the government described as a "credible deterrent" to protect its territorial integrity.

The navy has acquired two refurbished American coastguard frigates in the past two years, and they now lead patrols in the South China Sea.

The navy wants to acquire up to six more to guard the country's long coastline effectively, armed forces chief of staff General Emmanuel Bautista announced in January.

In 2012 the Gregorio del Pilar, one of the two refurbished frigates, confronted Chinese ships on Scarborough Shoal, a small outcrop just off the coast of the country's main island of Luzon.

The Chinese eventually gained control of the outcrop after Manila backed down. However, the Manila government sought UN arbitration to settle the dispute, a move rejected by China.

Last month the Philippines lodged a protest after the Chinese coastguard allegedly attacked Filipino fishermen off the shoal with water cannon on January 27. Beijing rejected the protest.

China claims nearly all of the South China Sea, including waters near the coasts of its neighbours.