Japan will loan the Philippines 64.38 billion yen ($413 million) to buy the five 97-meter Multi-Role Response Vessels and pay for the "development of the required support facilities", the foreign ministry said in a statement.
"This will support the PCG in improving its capabilities for maritime operations particularly in addressing transnational crimes," the statement said, referring to the Philippine Coast Guard.
Japan is a top provider of overseas development assistance to the Philippines.
The countries are seeking to deepen their security cooperation as China becomes more assertive in pressing its claims in the South China Sea.
Beijing claims almost the entire waterway, brushing off rival claims from other countries, including the Philippines, and an international ruling that its assertion has no legal basis.