Washington is willing to manage differences with Beijing in a constructive manner and avoid letting them affect bilateral ties, Biden was quoted in a Foreign Ministry news release as saying.
Biden said he believed Xi is a candid and constructive person.
"In developing this new relationship, both qualities are sorely needed," Biden said during the meeting.
"Candor generates trust," he said, adding that the US-China relationship must be "based on trust and a positive notion of each other's motives".
Biden and Xi have built good personal relations. During Biden's trip to China two years ago, Xi, then vice-president, accompanied him on a trip outside Beijing. Biden also accompanied Xi on his US trip in February 2012.
On Wednesday, Xi led high-ranking officials to meet Biden, and their talks lasted much longer than scheduled.
The air zone covers China's Diaoyu Islands, on which Japan also claims sovereignty. Japan and many other countries including the US established such air zones of their own decades ago.
Beijing has repeatedly said it is Japan that first changed the status quo in the region by "nationalizing" the Diaoyu Islands last year.
Foreign Ministry spokesman Hong Lei said on Wednesday that China has maintained communication with the US over the air zone issue.
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