The world number two said he had wanted to play but that after an MRI scan his doctors had advised him not to, BBC Sport reported.
"They say if I play here, there is a risk... to not have the chance to play Melbourne," he said in a statement.
The Spaniard, 32, missed November's ATP Finals to have ankle surgery, having also had an abdominal muscle problem.
Japan's Taro Daniel will replace Nadal in round two in Brisbane against Frenchman Jo-Wilfried Tsonga.
Nadal withdrew from an exhibition event in Abu Dhabi last week after losing his opening match to Kevin Anderson.
"I felt a little bit the leg, the tightening in Abu Dhabi," the 17-time Grand Slam singles champion said.
"I have to be ready to understand that this kind of stuff happens when you're coming back from injuries. I have to accept and keep going."
The Australian Open in Melbourne runs from January 14-27.