Captain Michael Clarke (lower back) is already facing a race against time to be fit for Australia's defence of the June 6-23 tournament in England, while injury-prone fast bowler Pat Cummins (upper back) appears set miss out completely.
Pattinson, who turns 23 next month, was undergoing the surgery in Melbourne and was expected to return to training in about a month, Cricket Australia (CA) said in a statement on Thursday.
"James Pattinson will be having surgery tomorrow for a non-cricket related medical condition in his lower abdominal region that has been troubling him during the latter part of the recently concluded tour of India," CA chief medical officer Justin Paoloni said.
"James has undergone tests and consulted specialists since returning from India, and it was felt that surgery is absolutely necessary at this time.
"The recovery time will be determined once the surgery is completed but James is expected to return to training in approximately four weeks.
"His preparation for the Ashes is not expected to be affected but his availability for the ICC Champions Trophy will be determined at a later stage."
Australia will remain in England for the Ashes series starting on July 10 with Nottingham's Trent Bridge hosting the first of five tests.