The staffer was allegedly involved in an incident on 12 March, but police were unable to question him after the embassy declined their request and have refused to give further details of the allegations..
New Zealand asked the US to remove the man, who American officials confirmed had left on Saturday.
According to the Police they were continuing to investigate the incident, which took place just outside Wellington.
All diplomatic staff working in New Zealand are immune from prosecution, thanks to the 1961 Vienna Convention.
However, New Zealand’s foreign ministry said it makes it “clear with all diplomatic missions in New Zealand that it expects foreign diplomats to abide by New Zealand law, and to waive immunity… if there are allegations of serious crimes”.
The US embassy in Wellington did not comment on the specifics of matters under investigation.
But added: “We take seriously any suggestion that our staff have fallen short of the high standards of conduct expected of US government personnel.”