The leader is the first head of state to be hosted by President Rodrigo Duterte.
In a joint news conference, Abe and Duterte announced plans to strengthen the two nations’ economic relations, and work together to bolster security in the region’s waters.
Abe also pledged to help the Philippines with infrastructure projects through the use of technology.
The prime minister’s visit is seen as a way to shore up ties with the firebrand president, whose unconventional foreign policy strategy includes moving away from traditional ally the United States and reaching out to China.
Manila’s position puts Japan in an uneasy position, given Tokyo’s warm ties with Washington and rivalry with Beijing.