The amount, part of a $204-million loan, will cover two patrol ships for the Philippine Coast Guard, which had received the first of an earlier 10-vessel loan, the Japanese foreign ministry said late Wednesday.
Japan said it would extend a $157-million (16.4-billion yen) loan to help boost the Philippines' maritime security as both countries agreed to elevate their ties to a "level higher than before" amid China's growing influence in the region.
The rest of the loan will fund an agribusiness project for the Autonomous Region in Muslim Mindanao, the ministry said.
"Both Japan and the Philippines are maritime nations and support to enhance maritime safety capability will be strengthened," said Japanese Prime Minister Shinzo Abe, who witnessed the signing of the agreements following a bilateral meeting with President Rodrigo Duterte on Wednesday.
The Philippines will also receive TC-90 trainer aircraft from Japan's Maritime Self-Defense Force.
Tokyo will also provide high-speed small vessels and other equipment to boost Manila's counter-terrorism operations, especially in the porous borders in the south.
Duterte told Abe on Wednesday that the Philippines would "work closely" with Japan to peacefully resolve sea disputes, without specifically mentioning China.
Manila and Tokyo are locked in separate disputed with Beijing in the South and East China Seas, respectively.