The Philippines hailed the start of major war games with the United States on Monday as a timely boost to their military alliance, amid a tense territorial dispute with China.

More than 6,000 Filipino and US soldiers will take part in the 12 days of exercises across the Philippines, which come as the host nation is embroiled in a dispute with China over rival claims to the South China Sea.

At an opening ceremony for the exercises in Manila, Philippines' armed forces chief Jessie Dellosa did not specifically mention China but said the war games highlighted strong US support for its weaker ally at a crucial moment.

"Given the international situation we are in, I say that this exercise, in coordination with all those we had in the past, (is) timely and mutually beneficial," Dellosa said in a speech.

"The conduct of this annual event reflects the aspirations to further relations with our strategic ally, a commitment that has to be nurtured especially in the context of the evolving challenges in the region."

China and Taiwan claim nearly all of the South China Sea, even waters approaching the coasts of the Philippines, Vietnam, Brunei and Malaysia.

The competing claims have for decades made the sea -- where there are shipping routes vital for global trade and which is believed to hold huge deposits of fossil fuels -- a potential flashpoint for military conflict.

While diplomatic efforts have kept the dispute from flaring into violence over recent decades, the Philippines and Vietnam said last year that China was becoming increasingly aggressive in staking its claim to the sea.

The Philippines accused Chinese vessels of firing warning shots at Filipino fishermen, harassing an oil exploration vessel and laying markers in areas close to Philippine landmass.

Tensions spiked again last week when the Philippines sent its biggest warship to a tiny shoal about 230 kilometres (140 miles) west of the county's main island of Luzon where eight Chinese fishing boats had been seen.

China deployed three vessels to stop Philippine personnel from arresting the fishermen, and the dispute escalated with both countries launching protests and trading accusations that the other was violating their sovereign territory.

While the fishing boats left Scarborough Shoal over the weekend, both nations are continuing to assert their sovereignty over the area, which is many hundreds of kilometres from the nearest major Chinese landmass.

Philippine President Benigno Aquino said Monday that Balikatan had nothing to do with the Scarborough Shoal dispute and there was no reason for the war games to provoke China.

However the Philippine military has confirmed some of the drills will be held just off the western coast of Palawan in waters facing the South China Sea.

The exercises are also being held as the United States is rebuilding its military presence across the Asia Pacific, partly to counter the growing political, economic and military might of China.

The director for the US side for Balikatan, Brigadier General Frederick Padilla, confirmed Monday the exercises were part of US President Barack Obama's military plan for the region.

"The president of the United States has stated that it is the desire of our country to be engaged more in the Pacific region -- that includes working with the Filipino government and the armed forces," he told reporters.

But Padilla insisted the exercises were not meant as a warning to China amid its dispute with the Philippines over Scarborough Shoal.

"This exercise is, from our stand point, not linked to any particular situation," Padilla said.

China, which has expressed irritation at the increased US focus on Asia, said Monday it was displeased with the war games.

"The major trend of the times in this region is peace and development. Military exercise does not represent the major call of the times," foreign ministry spokesman Liu Weimin said in Beijing.

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