"Cricket Australia has today advised that fast bowler Peter Siddle has suffered a stress fracture of his back," CA said in a statement.
Australia team physiotherapist Alex Kountouris said Siddle's injury was revealed in scan conducted after the five-match One-Day International series against Pakistan last week.
"Peter experienced back pain during the Commonwealth Bank Series. The source of the pain was investigated after the fifth ODI and unfortunately scans revealed that he has a lower back stress fracture," he said.
Siddle has also been forced out of Australia's domestic competition.
"The nature of this injury means that Peter will require a long rehabilitation period and as such he'll be unavailable for the remainder of the domestic summer and the tour of New Zealand," Kountouris said.
Australia's tour of New Zealand starts March 3 with a five-match ODI series to be followed by two Tests.