The announcement came days after China accused its Asian rival of interfering in the South China Sea (Vietnam's East Sea).
Japan, which occupied the Philippines and Vietnam during World War II, is now strengthening relations. All three countries share growing concerns about China's increasing military muscle amid a series of maritime disputes.
China claims almost all the South China Sea. It is also embroiled in a separate row with Japan over disputed islands in the East China Sea that has seen relations sour badly in recent years.
Tensions in the South China Sea - through which one-third of the world's oil passes - have mounted in recent months since China transformed contested reefs into artificial islands capable of supporting military facilities.
Brunei, Malaysia, Vietnam and Taiwan also claim all or part of the Spratlys chain in the sea, while Vietnam and Taiwan have rival claims with China in the Paracels chain there.
The Japanese submarine Oyashio and two escort vessels will visit Subic Bay in the Philippines for annual open sea drills, a spokesman for Japan's Maritime Staff Office confirmed to AFP. The escort ships will also subsequently visit Cam Ranh Bay in Vietnam.
The exercise, joined by some 500 personnel including officer candidates, is scheduled from Saturday through April 27.
It will be the first call at a Philippine port by a Japanese submarine since 2001, while the visit by the escort ships to Cam Ranh Bay will mark a first for Japan's navy, the spokesman said.
The submarine will not go to Vietnam, he said.
Beijing accused Tokyo of interfering in the South China Sea, known as the East Sea to Vietnam, after Manila said it would lease five Japanese military planes.
Philippine President Benigno Aquino said last week that Manila would lease five TC-90 training aircraft from Japan to "help our navy patrol our territory", pointing to the disputed South China Sea in particular.
China immediately reacted, saying it was "firmly opposed" to challenges to its sovereignty and security and would "remain on high alert". - AFP