The annual Kamandag, or Venom, exercises are focussed on defending the north coast of the Philippines' main island of Luzon, which lies about 800 kilometres (500 miles) from self-ruled Taiwan.
Beijing considers Taiwan part of its territory and has vowed it will never rule out using force to take it, calling Monday's drills a "stern warning" to "separatist" forces on the island.
The joint US-Filipino exercises also come days after a collision between a Chinese and a Philippine vessel in the South China Sea.
It was the latest in a series of confrontations between the two countries in the strategic waterway claimed almost entirely by Beijing.
Philippine Marine Corps commandant Major General Arturo Rojas stressed at Tuesday's opening ceremony in Manila that Kamandag was long planned and had "nothing to do with whatever is happening in the region".
The drills' primary focus will be live-fire exercises along Luzon's north coast, while other activities will be conducted on tiny Philippine islands between Luzon and Taiwan.
"It's a coastal defence doctrine. The doctrine says that a would-be aggressor might be directed towards our territory," Filipino exercise director Brigadier-General Vicente Blanco told reporters.
"We are not exercising to join the fight (over Taiwan)," he added.
US Marines representative Colonel Stuart Glenn said the exercises were aimed at helping the United States and its allies respond to "any crisis or contingencies".
The western Philippine island of Palawan, facing the South China Sea, will also host part of the drills.
The US and Philippines are fielding just over a thousand participants each, while smaller numbers of Australian, British, Japanese and South Korean forces are also taking part.
An amphibious landing and training on how to defend against chemical and biological warfare were also among the activities planned, according to a press kit.
As the war games began Tuesday, the Philippine government announced that the BRP Datu Cabaylo, a civilian patrol vessel, had sustained minor damage on October 11 when it was "deliberately sideswiped" by a "Chinese Maritime Militia" vessel.
The collision dented the 30-metre (98-foot) vessel's front right section, the Bureau of Fisheries and Aquatic Resources said in a statement.
It took place about 9.3 kilometres (5.8 miles) from Thitu, a Philippine-garrisoned island in the Spratly group.
Prior to the collision, the Chinese vessel also "conducted dangerous manoeuvres and tried to block the path" of the Filipino boat, which was conducting routine patrol, the bureau said.
The crew were unhurt and later sailed the vessel to Thitu.
"What they did to us is against international law and violates our sovereign rights in the West Philippine Sea," Nazario Briguera, the spokesman for the fisheries bureau, told AFP, using Manila's term for its claimed sections of the South China Sea.
He said the Datu Cabaylo was the third vessel owned by the bureau that was damaged in clashes with Chinese vessels this year.
Beijing has for years sought to expand its presence in contested areas of the sea, brushing aside an international ruling that its claim to most of the waterway has no legal basis.
China has in recent months deployed military, coast guard, as well as what the Philippines and its allies describe as "maritime militia" forces in a bid to eject the Philippines from a trio of other strategically important reefs and islands in the South China Sea.
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