The hero of England's Ashes-winning triumph last year is due to have surgery on his left ankle next week after an attempt at a comeback ended with him leaving the field after bowling just two overs against Kent on Friday.
England had hoped rest and rehabilitation would be the answer to a problem that had its origins in bone fragments left in Flintoff's left ankle from an operation at the beginning of last year.
But the man the selectors want to captain the team in Australia now faces a spell on the sidelines which could leave him desperately short of match practice before November's first Ashes Test in Brisbane.
For Atherton, a former Lancashire team mate of Flintoff, the situation has worrying echoes of England's last tour of Australia in 2002/03.
Back then England arrived with several players -- including Flintoff, Darren Gough, Simon Jones and Marcus Trescothick -- who were not fully fit.
Australia went on to retain the Ashes in a mere 11 days' playing time and won the series 4-1.
"It was a shambolic start to England's last Ashes tour and, on the back of that, the selectors were very clear when they said, 'We will not do this again, we will not take players who are not fully match fit'," Atherton told Sky Sports.
"But they are going to be faced with this situation with Andrew Flintoff, that here's a guy who's played minimal cricket for the best part of eight or nine months, but a guy they want to captain out there (Australia)."
"It's going to be an interesting question because he's going to be getting on that plane without any knowledge really that he's fully match fit," the former opener added.
"Going back to what happened four years ago that is exactly the situation the selectors were keen to avoid again, going out on a long, three-month tour of Australia.
"They said it wouldn't happen again but they are going to be faced with a tricky situation to justify somebody's inclusion."
And with Michael Vaughan, who led England to Ashes glory last year, also out of the return series, and fellow Ashes-winners Ashley Giles and Simon Jones both still sidelined, Atherton was adamant Flintoff's was not an isolated case.
"It does seem to me that over the last four or five years this has been a regular problem for England players.
"The management of injuries seems to be -- incompetent might be too strong a word for it -- recurring time and time again.
"You can go back to that Ashes series four years ago and move on from there and the number of players that have an operation, rehabilitation that seems to go all right but then they demand another operation -- Simon Jones, Ashley Giles, Michael Vaughan, Andrew Flintoff, Darren Gough -- it's a long list and I think some questions should be asked."
England used just 12 players in their 2-1 series win over Australia last year and selection chief David Graveney defended the present set-up.
"We've got a much more extensive medical team in place now than when I became chairman of selectors in 1997. But I think these questions are best addressed to the medical officer," he told AFP.
Peter Gregory, England's chief medical officer, was unavailable for comment Saturday as he was on annual leave and was not expected back at work until Tuesday.