The two-Test series " which begins in the United Arab Emirates next month " will see Australia return to the longest form of the game for the first time since a stunning 2-1 win against South Africa in February and March.
That series win catapulted Australia to the top of the Test rankings for the first time since 2009, although they have since been replaced at the summit by the Proteas.
But Clarke, who re-injured a troublesome hamstring in the recent one-day tri-series against South Africa and Zimbabwe, left the tour early for treatment.
The 33-year-old was still named in Australia's 15-man squad for the Pakistan series " announced on Monday " but when asked if he was confident that Clarke would play the first Test in Dubai next month, Marsh told a news conference: "No. Not confident. You can't be confident about Michael.
"But he's only missed one in over a hundred [Tests]. He's got a great track record of getting up for Tests.
"I'm sure he'll be right because there's no more dedicated bloke in getting his rehab in than Michael.
"He will not want to miss any Test matches, even if that means he has to miss some one-dayers and I'm not suggesting that.
"Being named in the one-dayers not only named but he's captain he'll try desperately to be ready for them.
"Whether or not he will be " I don't know."
Australia play one Twenty20 international and three one-day internationals against Pakistan in the Middle East before the Test series begins.