The 33-year-old suffered the problem during his side's recent triangular series in Zimbabwe.
The veteran batsman will now miss Australia's three ODIs versus Pakistan in the United Arab Emirates, though he could be back for the two Tests that are due to be played in late October.
"Since returning to Australia, Michael has had a series of investigations that have confirmed a significant hamstring injury," Cricket Australia physiotherapist Alex Kountouris said in an official statement.
"Importantly, the scans have demonstrated tendon damage - which complicates the recovery from this injury. As such, he will not recover in time to be available for the ODI series in the UAE.
"We hope he will be available for the Test series, but this will be determined at a date closer to the first Test."
Australia play their first ODI against Pakistan on October 7.