Stokes suffered a left hamstring tear in the build-up to the ongoing second Test against Pakistan at Headingley and was replaced in England's side for that match by debutant paceman Sam Curran.
"England all-rounder Ben Stokes will miss the ODI against Scotland in Edinburgh and will be unavailable for the first part of the five-match Royal London ODI series against Australia as he recovers from a left hamstring tear," said an ECB statement.
It added the 26-year-old will be "assessed later this week", saying Stokes will "continue his rehabilitation programme and will return to his county side Durham on Monday".
Middlesex batsman Dawid Malan has been drafted into the squad for the Scotland game in Edinburgh on June 10.
Meanwhile Kent batsman Sam Billings has been called into the squad for the series against Australia, which sees England, top of the International Cricket Council's ODI rankings, taking on the reigning 50-over world champions. That campaign gets underway at The Oval on June 13.
First Published: June 3, 2018, 10:12 PM IST