'Major setback' for the touring side as Atkinson leaves the field suffering a hamstring problem.
The English seamer increased England's injury problems after leaving the ground on the second morning of the Boxing Day Test versus the Australians.
The right-arm seamer pulled up with his hamstring after the final ball of the fourth over on Saturday.
The touring camp reported Atkinson had experienced "tightness" and was to take time off the field for further assessment "over the next few hours".
The concluding match of the series in Sydney gets underway at the end of the week.
The visitors have previously lost key quicks Mark Wood to a knee injury and another paceman with an abdominal strain during this series.
A replacement bowler was brought into the squad to provide backup.
The seamer had a tough time in the opening two Tests, claiming a mere a handful of scalps.
He was dropped for the Adelaide match, before being recalled for the Melbourne Test as Archer's replacement.
The county bowler performed better in the fourth Test, claiming a couple of wickets during the host's first knock, and scoring 28 runs while batting as one of just three England players to reach double figures.
Post a single over in Australia's second innings, he returned on Saturday morning and removed Scott Boland taken by the wicketkeeper.
Unfortunately, at the end of his spell, he sent down a variation to the batsman and promptly felt for his hamstring.
Gus Atkinson was brought back for the Melbourne match after being left out the previous Test.
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