Starc, who has had trouble with his right ankle stemming back to the Ashes series in England this year, suffered a stress fracture of the same foot in the day-night third Test against New Zealand in Adelaide late last month.
It has now been decided he needs ankle surgery meaning Starc will miss the remainder of the Australian season.
"After discussions with specialists, and in consultation with Mitchell, we believe the best course of action would be for Mitchell to have the surgery for his ankle impingement now while he is currently laid off with the stress fracture in his foot," CA physiotherapist David Beakley said in a statement.
Left-armer Starc, 25, is Australia's leading strike bowler and has taken 91 wickets in 25 Tests at 30.58.
He also bowled the fastest-recorded Test delivery of 160.4 kilometres per hour (99.7mph) during the drawn second Perth Test.
A date for surgery is yet to be confirmed. The World T20 takes place in India in March-April 2016.
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