A spokesman said Clarke had left the team hotel in Hamilton on the eve of today's third one-day international against the Black Caps and it was not known when he would return.
Clarke's fiancee, Lara Bingle, has announced she is suing AFL player Brendan Fevola over a nude photo she claims Fevola took without her permission.
Woman's Day last week published the photo of Bingle in the shower which was allegedly taken while she and Fevola were involved in a secret affair in 2006.
Bingle has opened up in a magazine interview about the release of the photo, saying she has been deeply humiliated.
Bingle told the magazine the nude photo was taken without her permission and she felt exploited and compromised by its release.
The model says she is suing the footballer to restore her "dignity and self-respect".
Clarke's departure leaves the Australian one-day squad down to just 12 players, with paceman Clint McKay and all-rounder Adam Voges vying for a place in the side with Clarke gone.
A replacement player may be called up from Australia for the final two one-day games, in Auckland on Thursday and Wellington on Saturday, a spokesman said.
It is not known if Clarke will return for the two-test series starting on March 19.
