The war games, which began Monday in Palagan, follow a standoff between Chinese and Philippine vessels in Scarborough Shoal in the Spratly Islands, where Philippine navy personnel tried to stop Chinese fishing vessels from harvesting corals, sharks and fish, The Philippine Star reported.
"This will not result in provocation. As we have said, the exercises have long been scheduled and these have nothing to do with the incident," deputy presidential spokeswoman Abigail Valte said on state-run radio dzRB.
The military exercises are to continue through April 27.
The Manila Bulletin reported the standoff came after the Philippine navy attempted to arrest Chinese fishermen caught poaching at Scarborough Shoal and two Chinese surveillance vessels prevented the arrests.
"The concentration is how to solve the incident through diplomatic means," Valte said.
Valte said the Philippines government has not abandoned its claims in the region, which lies within the country's 200-mile exclusive economic zone, and the government will maintain its claim, jurisdiction and authority but will seek a diplomatic solution.
China claims the entire South China Sea as a historic right, including waters near the coasts of the Philippines and other Southeast Asian countries. Other countries in the region also claim parts of the islands.
Amid what is seen as a growing threat from China, President Benigno Aquino III called last year for closer military ties with the United States but not a return to permanent U.S. bases in the Philippines.
U.S. officials have sought to increase the U.S. presence in the Asia-Pacific region in the face of the increasing political, economic and military strength of China.