Beijing claims almost the entire disputed waterway, through which more than 60 percent of global maritime trade passes, despite an international ruling that its assertion has no merit.
The "maritime cooperative activity" was held Tuesday in waters off Palawan and Occidental Mindoro in the western Philippines.
The two countries' coast guards have held joint exercises before, but never as part of combined military drills which Manila's armed forces said reflected a "growing whole-of-nation approach to maritime cooperation".
The Philippine coast guard deployed its 97-metre (320-foot) ship BRP Melchora Aquino and 44-metre ship BRP Malapascua while the US coast guard used the cutter Stratton, the Philippine military said in the statement.
The coast guard vessels joined Philippine navy and air force assets and US navy P-8A Poseidon maritime patrol aircraft in a series of exercises including communication checks, search and rescue and division tactics.
"As the Philippines continues to navigate evolving maritime challenges, joint activities like the MCA reaffirm the (Philippine military's) commitment to modernizing its capabilities and strengthening defense partnerships to secure our national and regional maritime interests," Philippine military chief General Romeo Brawner said.
China's embassy in Manila did not immediately respond to AFP's request for comment.
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