Clarke, who was originally selected as vice-captain for the three-match tour, missed today's series opener in Wellington after feeling pain in his hip the previous day.
Australia's physiotherapist Alex Kountouris said Clarke would not recover in time to play in the remaining two matches and had been sent home as a precaution to ensure he was available for the World Cup, starting in the West Indies next month.
''Michael is still suffering some hip soreness in certain movements and has not progressed to the point where he is able to play a part in the Chappell-Hadlee Trophy,'' Kountouris said in a statement.
''As such, he will return to Sydney tomorrow (Saturday) to allow sufficient time to recover and is expected to be fully fit in time for the beginning of the 2007 ICC Cricket World Cup.'' Phil Jaques had already been called into the squad as a replacement for Clarke, one of four Australian World Cup players under an injury cloud.
All rounder Andrew Symonds is recovering from bicep surgery and will miss at least the first half of the World Cup, captain Ricky Ponting pulled out of the New Zealand trip with a back problem and fast bowler Brett Lee was sent home after injuring his ankle.
New Zealand thrashed Australia by 10 wickets in today's series opener. The second match is in Auckland on Sunday.