The Philippines insists the exercises, involving 4,500 US personnel and 2,300 Filipino troops, should not be seen by China as a provocation.
"Our aim is not against any country, our aim is to protect maritime security and to protect the interests of our country," Major Emmanuel Garcia, Philippine military spokesman for Balikatan, told AFP.
Nevertheless, Garcia confirmed US and Philippine ships will stage drills in waters facing the South China Sea, while Filipino leaders have repeatedly said that China is one of the country's main "maritime security" concerns.
China claims all of the South China Sea as a historic right, even waters close to the coasts of the Philippines and other Southeast Asian countries.
The competing claims to the strategically vital waters have long made the area one of Asia's potential flashpoints for military conflict.
The Philippines has complained over the past two years that China has become increasingly aggressive in staking its claim to the waters, accusing the Chinese of acts such as firing warning shots at Filipino fishermen.
Tensions spiked again this month when Philippine and Chinese ships became locked in a standoff at a tiny set of islets called Scarborough Shoal in the South China Sea.