China claims most of the strategic waterway despite an international ruling that its assertion has no legal basis.
Friday's exercises were held days after the Filipino coast guard expressed alarm over Chinese patrols moving closer to Manila's shores.
"While conducting sovereignty patrol in the West Philippine Sea, several offshore combat ships of the Philippine Navy held a unilateral exercise," a navy statement said, using the Filipino name for areas of the South China Sea claimed by Manila.
The "routine" exercise was "aimed at sustaining and improving the operational proficiency of both assets and personnel particularly in the vicinity of Bajo de Masinloc", it said, using the local name for a fish-rich reef called Scarborough Shoal.
This is "crucial in the fulfillment of the Navy's mandate of securing the seas and upholding the nation's territorial integrity".
Seized by China after a 2012 standoff with the Filipino navy, the reef is a key flashpoint of escalating confrontations between the Chinese and Filipino coast guards.
The confrontations have sparked concern they could draw the United States, Manila's long-time security ally, into armed conflict with China.
Friday's manoeuvres involved some of the Filipino navy's largest ships -- the frigate BRP Antonio Luna and the patrol vessels BRP Ramon Alcaraz and BRP Andres Bonifacio.
A navy spokesman told AFP they trained "in the vicinity south of Bajo de Masinloc".
The navy released video footage of uniformed crew firing a machine gun mounted on the side of a warship, and one of the vessels dramatically sweeping past a wall of white smoke that trailed a hail of bullets falling into the water.
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