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.
"Aggressive patterns of behaviour aimed at changing the status quo threaten peace and stability in the region."
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".
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.
About 2,500 US soldiers are joining 3,000 Filipino troops in the manoeuvres, which began a week after Obama assured Manila his government was committed to a 1951 mutual defence treaty.
- Meet 21st century challenges -
Also last week, the allies bolstered their security alliance with a new defence agreement giving American forces greater access to Philippine bases -- part of a US rebalancing towards rising Asia.
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.
Obama's four-nation Asian tour was dominated by worsening maritime tensions between Beijing and Washington's allies in the region, which have triggered fears of military conflict.
The Philippines, which has one of the weakest militaries in the region, has repeatedly called on the United States for help as China has increased military and diplomatic pressure to take control of the contested areas.
While Obama sought to reassure the Philippines that the United States would support its ally in the event of an attack, he did not specifically mention coming to the aid of Manila if there were a conflict over the contested South China Sea areas, as his hosts had hoped.
But he ended his trip with a warning to China against using force in territorial disputes.
Obama's trip drew a frosty response from Beijing, with Chinese authorities accusing the US president of ganging up with "troublemaking" allies.
Philippine military spokesman Lieutenant-Colonel Ramon Zagala said the war games would feature live-fire drills, search-and-rescue operations and humanitarian response scenarios in several locations.
There will also be demonstrations of maritime surveillance systems and ship-to-shore landing exercises in Zambales province, three hours' drive north of Manila and facing the South China Sea, Zagala said.