The 27-year-old, who was recalled into the team after shoulder surgery ruled him out of the squad a year ago, sustained a calf strain during a Big Bash League (BBL) clash with the Perth Scorchers last week.
Confirming the news, CA's head of sports science Alex Kountouris revealed that Chris initially complained the tightness in his calf during the domestic T20 match and now, the scans have confirmed that he was expected to remain out of action for three-to-four weeks.
"Chris initially left the field against the Scorchers complaining of tightness in his calf. He reported increasing discomfort over the 24 hours that followed and the Heat's medical staff made the decision to send him for a scan.
That scan confirmed the injury, which is expected to prevent him from playing for three-to-four weeks," ESPNcricinfo quoted Kountouris, as saying.
"When Chris recovers, the expectation is that he will need to prove his fitness in match action before being considered again for international selection," he added.
The calf strain is the latest setback for Lynn, who had sustained a shoulder injury while on national duty last summer before he was forced to miss the start of this year's BBL due to a hamstring problem.
And Lynn said that though he was quite disappointed to miss an opportunity with the ODI side, he would work on his fitness to be back in action as soon as possible.
"It is annoying and I'm very disappointed to miss an opportunity with the ODI side, but I know it is minor in the scheme of things. I have been working very hard to get myself right, and the positive thing is that my shoulder is feeling very good. I'll do the work again and I am confident I will give myself a shot at playing some good cricket again soon," he said.
Though the Australian selectors are yet to name Lynn's replacement, the injury could open the door for Maxwell, who was controversially dropped from the national squad last week for the first time since his debut in 2012-13.
The five-match ODI series between the two Ashes rivals is slated to begin on January 14 at the Kennington Oval in London.
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