The 26-year-old has been struggling with a right shoulder problem for more than a month and the Croatian skipped the Brisbane International in the hope of recovering in time for the season's first Grand Slam beginning in Melbourne on Jan 19.
"I am really disappointed to announce that I had to withdraw from the Australian Open," Cilic said in a statement on his website (www.marin-cilic.net).
"I was advised by doctors to be careful as much as possible to avoid even more serious problems.
"It is improving day by day, but I still don't feel fit enough to be able to compete at the highest level."
Image: Marin Cilic
Photograph: Clive Brunskill/Getty Images
Radwanska downs Serena in Hopman Cup final
Golden Globe 2015: The awards that will go WRONG
Wrist injury rules Del Potro out of Brisbane event
Federer beats Dimitrov to reach Brisbane final
BCCI eyes October-January window for home matches