Clarke missed the start of his side's one-day tri-series tour against South Africa and Zimbabwe with a left hamstring problem.
He returned to the fold on Sunday but could not stop his side falling to a shock loss against Zimbabwe in Harare.
Clarke retired hurt during his innings of 68 not out, only to later return, while he also bowled an over, but Zimbabwe were still too good as they claimed their first one-day win against Australia since 1983.
And Clarke - who was quick to pay credit to Zimbabwe - confirmed his injury was serious, placing him in doubt for Australia's tour of the United Arab Emirates, where they will face Pakistan, in October and November.
"The hamstring's not great," Clarke said.
"Unfortunately I've done it again. I'll be on a plane back to Australia in the next 24 hours to try and get it fixed."
When asked if his side had not scored enough - they made just 209-9 in their 50 overs against Zimbabwe - Clarke emphatically agreed, saying: "No. Definitely not enough runs.
"I think credit needs to go to Zimbabwe. I thought they bowled really well and their batting was outstanding.
"Maybe up front [today] I thought there would have been a bit of spin, but not throughout the whole game.
"And I think that's where we lost the game."
Australia have now lost two one-day matches in a row and will need to beat South Africa in Harare on Tuesday to guarantee their place in the tournament final.