A Philippine-flagged cargo ship sank off an island in the centre of the country, leaving one crew member dead and two others missing, the Coast Guard said on Tuesday.

The Jerlyn Kathness was taken down by big waves in the San Bernardino Strait off the island of Samar on Monday, with passing vessels rescuing 11 of the 15 crew members overnight, Coast Guard station commander Bryhl Amay told AFP.

After more than 25 hours in the water, another crew member managed to swim ashore to the tiny island of San Juan before dawn Tuesday.

Fishermen retrieved the body of another crew member off the island of Biri, Amay added.

A search for the two still missing crew members was underway Tuesday, Amay said.

The vessel was ferrying 24 tonnes of cement to Samar from the central island of Cebu.

The official could not immediately provide other details about the sunken vessel, which a tracking website described as a 199-tonne general cargo ship built in 1993.