Biden's tour of northeast Asia, which will also take him to Beijing and Seoul, comes as tensions in the region are at their highest for years, with China and Japan squaring off over a chain of uninhabited islands in the East China Sea.
Nerves are particularly frayed after Beijing's proclamation of an Air Defence Identification Zone over the sea, including the disputed islands, in which it says all aircraft must obey its orders on pain of unspecified "defensive emergency measures".
"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 ahead of Biden's one-on-one with Prime Minister Shinzo Abe.
"I think they will confirm that Japan and the United States will keep closely cooperating on this issue," he said.
"Japan and the United States share the position that China's ADIZ is unacceptable... I think (Biden) will head to China to discuss various issues including this, with his understanding of Japan's position," Suga said.
Beijing's announcement of the ADIZ provoked fury in Tokyo, Seoul and Washington, who all sent military or paramilitary planes into the zone in defiance of Chinese orders.
In Washington, senior administration officials said Biden, who is expected to meet Chinese President Xi Jinping in Beijing later this week, plans to convey Washington's "concerns" to China and seek clarity regarding its intentions.
Analysts are divided over whether it was a clever long-term move by Beijing in its bid to undermine Japan's claims to control the disputed islands, or an over-reach by an administration that doesn't fully appreciate its impact.
Abe will be looking for Biden to bolster his position that China is being unreasonable and aggressive, said Takehiko Yamamoto, professor of international politics at Waseda University in Tokyo.
"But at the same time, Washington does not want to take the risk of damaging its bilateral ties with China," he said.
"Biden will deliver the message to the Chinese side but may also seek to play a role in mediating," he added.
Analysts point out that Tokyo and Washington appear at odds over instructions to their airlines flying through the zone, with Japan telling its carriers they should not comply and the US advising American companies that they should.
After a morning coffee with Irish premier Enda Kenny, who is staying at the same hotel on a five-day visit to Japan, Biden went to the US embassy where he met with new ambassador Caroline Kennedy and Japanese Deputy Prime Minister Taro Aso.
He is expected to meet Crown Prince Naruhito later in the day before a formal meeting and dinner with Abe.
Biden will move to Beijing on Wednesday to hold talks with Xi before flying to Seoul, where he is to meet South Korean President Park Geun-Hye.
President Barack Obama pledged in his first term to "pivot" US foreign policy toward Asia.
But he called off a trip to the region in October to negotiate with Republicans who shut down the US government in a failed bid to stop his signature health care reform.
Biden's visit is intended to help re-affirm US commitment to the region, ahead of an intended trip to Asia by Obama in April.