The 32-year-old fast bowler has been ruled out of upcoming white-ball series against New Zealand and India after scans revealed signs of lumbar bone stress.
Cricket Australia (CA) confirmed on Tuesday that Cummins had lingering back pain from the West Indies tour and the injury would require ongoing management in the lead-up to the five-test Ashes against England starting on November 21 in Perth.
"Cummins won't be considered for the upcoming limited-overs series against India or New Zealand and will continue his rehabilitation plan with a return to bowling to be determined as part of his Ashes preparation," CA said in a statement.
Cummins has already been rested from a number of white-ball fixtures, including home Twenty20 and One Day International series against South Africa.
While the injury has not been classified as a stress fracture, it is an echo of the back concerns that hampered his early career.
Cummins had to wait over five years for a second test following his stunning 2011 debut against South Africa when he took seven wickets in Johannesburg as an 18-year-old.
Since his return in 2017 he has become one of Australia's most durable players, missing just two tests through injury during his tenure as captain.
His absence would be a major blow to Australia's Ashes hopes, despite Victoria paceman Scott Boland being a worthy stand-by option.
Cummins has taken 91 wickets against England from 19 tests at an average of 24.10.
In nine tests on home soil, he has been even more devastating, taking 44 wickets at an average of 21.50.
Cummins' injury was revealed on the same day his long-standing pace teammate Mitchell Starc confirmed his retirement from T20 internationals, six months out from the T20 World Cup in India and Sri Lanka.
Of Australia's great pace triumvirate, only Josh Hazlewood will join the T20 squad for the three-match series against New Zealand starting on October 1 in Tauranga.
Left-armer Ben Dwarshuis joins Hazlewood and Sean Abbott among the pacers, with Nathan Ellis missing the tour for the birth of his first child.
All-rounder Cameron Green was omitted from the 14-man squad named on Tuesday and will continue his preparations for the Ashes and a return to bowling in the domestic Sheffield Shield.
However, all-rounder Marcus Stoinis earned a recall and is back in the World Cup frame.
Fellow all-rounders Mitch Owen and Matt Short were selected after recovering from concussion and a side strain respectively.
Australia T20 squad v New Zealand:
Mitchell Marsh (c), Sean Abbott, Xavier Bartlett, Tim David, Ben Dwarshuis, Josh Hazlewood, Travis Head, Josh Inglis (wk), Matt Kuhnemann, Glenn Maxwell, Mitchell Owen, Matthew Short, Marcus Stoinis, Adam Zampa