The agreement comes at a time when Manila and Tokyo share concerns about Beijing's growing assertiveness in the region.
Japan and the Philippines have signed a defence pact allowing troops to be deployed on each other's soil amid shared concerns over China's growing military power.
Japanese Foreign Minister Yoko Kamikawa and Philippine Defense Secretary Gilberto Teodoro signed the Reciprocal Access Agreement on Monday during a ceremony in Manila.
Under the agreement, Japanese forces will be allowed to deploy to the Philippines for joint military exercises and Philippine forces will be allowed to conduct combat training in Japan.
The pact must be ratified by the legislatures of both countries to enter into force.
The deal comes at a time when Japan and the Philippines, both long-standing US allies, are wary of China's growing assertiveness in the region.
Beijing has claimed more than 90 percent of the South China Sea, including waters within the exclusive economic zones of the Philippines and four other Southeast Asian countries.
In 2016, an international tribunal in The Hague found that Beijing’s claims had “no legal basis.”
The Chinese and Philippine coast guards and navies have been involved in numerous clashes in the disputed waters, including an incident last month during which Chinese coast guard personnel, armed with knives and spears, used speedboats to ram two Philippine navy supply vessels.
Japan has a long-standing territorial dispute with China over the Senkaku Islands located between Taiwan and Okinawa.
Under the leadership of Japanese Prime Minister Fumio Kishida, Tokyo has sought to increase its military firepower, including through reciprocal access agreements with Australia and the United Kingdom.
Philippine President Ferdinand Marcos Jr. has strongly denounced China's actions in the South China Sea and warned that his country would consider the death of any Filipino at its hands to be something close to “an act of war.”
Manila has long-standing defense pacts with Australia and the United States and is exploring a similar deal with France.
In April, the leaders of the United States, Japan and the Philippines held their first trilateral summit in Washington, DC, as part of efforts to boost military cooperation between the sides.
The summit came on the heels of joint military exercises in the South China Sea in which Australia also participated.
