Filipino Foreign Secretary Albert del Rosario said the 10-day drills were necessary to deal with the challenge of "aggressive" neighbours intent on "changing the status quo".
He did not mention China directly, but it has been robust in its efforts to assert territorial claims over most of the South China Sea, putting a strain on its relationships with neighbouring countries.
"In recent years tensions in the Asia-Pacific region have increased due to extensive and expansive maritime and territorial claims undermining the rule of law," del Rosario said at the opening ceremony.
He added that the military exercise, known as Balikatan (Shoulder to Shoulder), with its focus on "maritime capability" boosted the Philippines ability to "address these challenges".
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The Philippines last year asked a United Nations arbitration tribunal to declare what Manila said was Beijing's claim to 70 percent of the South China Sea as illegal and a threat to freedom of navigation.
The waters are believed to contain huge deposits of oil and gas and sit close to vital sea lanes.
Beijing has rejected UN arbitration and urged Manila to settle the dispute through bilateral talks instead.
The accord gives US forces, vessels and equipment increased access to certain Filipino bases over the next 10 years.
"The (new agreement) updates and strengthens US-Philippine defence cooperation to meet 21st century challenges," US ambassador to the Philippines Philip Goldberg said in a speech.