Left-armer Starc was last week ruled out the one-day series in England with lower back soreness and scans have now revealed the onset of stress fractures.
Cricket Australia chief medical officer Justin Paoloni indicated the 12-Test speedster is facing a long stint on the sidelines to recover.
"Mitch Starc had scans following his arrival back to Australia and they have shown an early stage low back stress fracture," Dr Paoloni said.
"His management plan will be determined in the coming days but he is expected to be unavailable for a prolonged period."
Starc joins fellow young guns James Pattinson and Pat Cummins on the long-term injured list with stress fractures, while Jackson Bird is also struggling to return in time with his own back injury.
Of Australia's top six Test quicks, only workhorse Peter Siddle is currently fit.
Ageing spearhead Ryan Harris is sidelined by a hamstring strain but is expected to be back in time for the first Test at the Gabba, starting November 21, unlike the young quartet.
The depth and quality of fast bowlers was to be Australia's strength for the series but now Clarke and coach Darren Lehmann must fall back on seasoned quicks like Mitchell Johnson and Clint McKay, whose best form has been in one-day cricket.
Starc, 23, was last week the third pacemen sent home from Australia's tour of England with a back injury, and scans on Monday revealed the serious nature of the problems.
"(Scans) have shown an early stage low back stress fracture," Cricket Australia medic Dr Justin Paoloni said. "His management plan will be determined in the coming days but he is expected to be unavailable for a prolonged period."
CA released a more positive update about Bird but Dr Paoloni admitted further scans were required to confirm the 26-year-old would be available some time during the Ashes series.
Cummins, 20, was not a member of the Ashes squad which lost 3-0 but had loomed as Pattinson's replacement, following the Victorian's injury in the Lord's Test, before suffering a recurrence of his own back troubles on Australia A's tour of Africa.
CA team general manager Pat Howard moved quickly to play down the cause of the injury crisis at a time Australia is relying more on rising quicks.
"While it's a disappointing result for Mitch, we know he will bounce back," Howard said. "Starc, James Pattinson and Pat Cummins are all under 24 years of age and we are certainly well aware that until fast bowlers get into their mid-20s they are more susceptible to injury.
"Historically, we've rarely seen three such promising young fast bowlers come through at the same time and all of a similar age so when they get injured of course that will be disappointing.
"Looking at a comparison of some of Australia's best quicks at the age of 23, Pattinson and Starc are second and third on the list behind Craig McDermott in terms of performance."
McDermott had 80 wickets in 24 Tests at 23, while Pattinson has 47 from 12 and Starc 41 from 12.
Dennis Lillee, who suffered back problems of his own, had played less Tests at 23 (nine) but boasted a better record with 47 scalps.
AUSTRALIA'S LIST OF INJURED QUICKS 10 WEEKS BEFORE THE RETURN ASHES SERIES
MITCHELL STARC - back stress fractures - will miss "prolonged period"
JAMES PATTINSON - back stress fractures - to return during domestic season
PAT CUMMINS - back stress fractures - to miss season
JACKSON BIRD - lower back injury - to return during Ashes
RYAN HARRIS - hamstring strain - to return late October