Tokyo said it was confident it would get US backing for its opposition to what it called an "extremely dangerous" move by Beijing, which asserted rights to control aircraft over a swathe of the East China Sea including disputed islands.
"We remain deeply concerned by the announcement of a new Air Defence Identification Zone (ADIZ)," Biden told the Asahi Shimbun before his tour of Northeast Asia, which will also take in China and South Korea.
Tensions in the region are at their highest in years with China and Japan squaring off over a chain of uninhabited islands in a feud that has some observers warning of the danger of an armed confrontation.
Nerves are particularly frayed after Beijing's proclamation of the ADIZ, in which it says all aircraft must obey its orders or risk unspecified "defensive emergency measures".
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"China's declaration of an air defence identification zone is an attempt to unilaterally change the status quo, which can invite unexpected situations and is an extremely dangerous act," Japan's Chief Cabinet Secretary Yoshihide Suga told reporters before Biden's one-on-one with Prime Minister Shinzo Abe.
Beijing's announcement of the ADIZ provoked anger in Tokyo, Seoul and Washington, which all sent military or paramilitary planes into the zone in defiance of Chinese orders.
The shared reaction in Japan and South Korea marked a rare moment of harmony in a relationship marked by constant friction over history and a separate set of contested islands. This hobbles US attempts to bring its two chief regional allies together.