Japan will lease a total of five surplus Beechcraft TC-90 planes to the Philippines, according to Manila's defence secretary Delfin Lorenzana.
Philippine military chief General Eduardo Ano said the new planes would be deployed over Benham Rise and the South China Sea.
Japan's attempt to bolster defence cooperation with Manila comes at a time of heightened regional concern over China's activities in disputed waters.
"As we are faced with many security-related issues in the Asia-Pacific, including those in the South China Sea, our cooperation with the Philippines for the regional security and stability is now even more significant," Japanese Defence Minister Kenji Wakamiya said at a ceremony to hand over the planes.
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China claims most of the sea, including waters close to the Philippine coast, despite the claim being declared as without basis last year by a United Nations-backed tribunal.
Beijing opposed the Philippines' lease of the planes almost as soon as it was announced last year under Manila's then-president Benigno Aquino, who took a tough stance on China's territorial ambitions.
However, Aquino's successor President Rodrigo Duterte has reversed this stance, openly courting China for trade and aid, while playing down the South China Sea dispute.
He also brushed aside concerns over Chinese survey ships that had been seen near Benham Rise -- waters east of the main Philippine island of Luzon that have been recognised by the United Nation as indisputably Philippine territory.
Parts of the South China Sea are also subject to competing claims by Brunei, Malaysia, Taiwan and Vietnam.