'Significant concern' for the touring side as Atkinson leaves the field suffering a hamstring problem.
The pace bowler increased the fitness woes of the England squad after leaving the playing area during Saturday's play in the Melbourne Test in the Ashes series.
The right-arm seamer felt a problem in his hamstring immediately following a delivery of the fourth over on Saturday.
The England team reported the 27-year-old reported "discomfort" and would spend time off the field in order to be assessed "during the day".
The series decider of the tour at the SCG starts at the end of the week.
England have previously lost strike bowlers Mark Wood to a knee injury and another paceman with an abdominal strain on the current trip.
A replacement bowler was added to the party as cover for Wood.
His form was underwhelming early in the series, managing only three wickets.
He was left out for the Adelaide match, then recalled for the fourth Test as Archer's replacement.
Atkinson performed better in the fourth Test, bagging two scalps with the ball, before adding 28 with the bat as one of just three English batsmen to get into double digits.
Post a single over at the end of day one, he resumed the next day and had nightwatchman taken by the wicketkeeper.
Unfortunately, on the final ball of that over, he bowled a variation to Travis Head and immediately felt for his hamstring.
Gus Atkinson was recalled for the Melbourne match after being left out of the third.
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