Manila announced the project after a visit by Japanese Prime Minister Fumio Kishida, who pledged in a speech that Japan would "continue to contribute to the enhancement of the Philippines' security capabilities".
The Philippines has been upgrading its maritime security assets and boosting ties with allies to counteract China's aggressive actions in the South China Sea, including areas disputed by the two neighbours.
Economic Planning Secretary Arsenio Balisacan told reporters the five 97-metre (318-foot) vessels will be delivered between 2027 and 2028, with funding worth 29.3 billion pesos ($525 million) loaned from Tokyo.
"The project will enable the coast guard to secure important sea lines of communication in the West Philippine Sea," among others, he said, using the Philippine name for its claimed areas in the South China Sea.
"It will also help the Philippine Coast Guard combat illegal activities and enforce maritime laws in the Philippine waters," he said.
China claims almost the entire South China Sea, through which trillions of dollars in trade passes annually, and has ignored a 2016 international ruling that its assertion has no legal basis.
Beijing deploys hundreds of coast guard and other vessels in the disputed waters to enforce its claim.
Japanese official development assistance has played a key role in upgrading the capability of the Filipino coast guard.
Tokyo in recent years has financed the acquisition of two of the agency's 97-metre, and 10 of its 44-metre, patrol vessels.
During the Manila visit last week, Kishida also announced Tokyo will provide the Philippines with a coastal radar surveillance system.
He and Philippine President Ferdinand Marcos also agreed to start negotiations for a defense pact that would allow the countries to deploy troops on each other's territory.