Mitchell Marsh will miss Australia's Twenty20 international against Pakistan in the VB Tour of the UAE opener on Monday (3am AEDT)and is unlikely to play in the ODI series following after picking up a hamstring injury playing for Perth Scorchers in the Oppo Champions League Twenty20.

Marsh now faces an anxious wait as to discover the full extent of the injury, which is complicated by surgery to the same left hamstring two years ago, with Cricket Australia seeking expert opinion from specialists, including the original surgeon.

Marsh "felt a pinch" in the field while captaining the Scorchers in their final CLT20 group game on Tuesday night and spent eight overs off the field before returning.

He later blasted 63 with the bat, including consecutive sixes to finish the game.

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Australia team physiotherapist Alex Kountouris said Marsh complained the injury had worsened after the flight from India to Dubai and was sent for scans, which revealed that he had appeared to have torn scar tissue on the upper left part of his hamstring.

"He's not playing the T20 and he's unlikely to be OK for the one-dayers," said Kountouris.

"The timelines are just too tight and we're probably not going to have a crack at it I don't think.

"He's moving around OK and seems OK. We'll wait and see for the Test matches how he progresses. There's certainly enough time for the Test matches.

"It's just a matter of getting his bowling back up, that's going to be the tricky part."

The first Test against Pakistan starts on October 22, with the team scheduled to play a four-day warm-up match in Sharjah starting on October 15.

Kountouris said if Marsh's injury is confined to the scar tissue it would work in the 22-year-old's favour, describing it as "not a bad outcome".

"Trying to decipher what's new, what's old, what's abnormal, what's normal is a bit hard," said Kountouris.

"So we're getting some opinions from back home from the guy who did the surgery, just to double-check with what we're doing.

"The consensus is that he's only torn the scar tissue but we're still looking into it.

"If that's the only thing that's happened it's going to be a sort of mild hamstring strain.

"It might get better really quickly or it might get better very slowly. That's what we don't know because of the unique nature of the injury."

Marsh joined his Australia teammates at the ICC Academy for a training session under lights on Thursday night, but did not take part in any activities.

Kountouris said his recovery was hard to predict but said he would "definitely be ready as a batter before he's ready as a bowler".

Marsh's injury leaves 12 fit players from the original 14-man ODI squad in early September, including Mitchell Johnson who is on track with his recovery from a rib injury and trained with the rest of the squad in Dubai on Thursday night.

Hobart Hurricanes' elimination in their CLT20 semi-final means Cameron Boyce (T20) and Ben Hilfenhaus (Test) are expected to link up with the squad on Friday, while left-arm orthodox spinner Stephen O'Keefe arrived late on Wednesday night.

With the rest of the Test players – Alex Doolan, Peter Siddle and Chris Rogers – set to arrive on Sunday, the team has plenty of cover available.