Manila is seeking to strengthen ties with Tokyo as tensions mount over the disputed waterway, almost all of which is claimed by China.
Japanese submarine Oyashio and destroyers JS Ariake and JS Setogiri docked in the Subic port Sunday for a routine visit at a sprawling former US naval base just 200 kilometers (125 miles) from a Chinese-held shoal.
"The visit is a manifestation of a sustained promotion of regional peace and stability and enhancement of maritime cooperation between neighboring navies," Philippine Navy spokesman Commander Lued Lincuna said.
The Ariake was equipped with an anti-submarine helicopter, according to an AFP photographer at the scene.
The port call came on the eve of war games between the United States and Filipino soldiers in the Philippines, which is seen as a showcase of a long-standing military alliance that the Philippines is counting on to deter China.
Seriously outgunned by its much larger rival China, the Philippines has turned to allies like the United States and Japan to upgrade its armed forces in recent years.
In February, Japan agreed to supply the Philippines with military hardware, which may include anti-submarine reconnaissance aircraft and radar technology.
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.
Aside from the Philippines, Vietnam, Brunei, Malaysia and Taiwan also have overlapping claims.
Japan and China are locked in a separate dispute over an uninhabited island chain in the East Sea.
The Philippines has asked a United Nations-backed tribunal to declare China's sea claims as illegal and the government expects a decision this year.