England captain Andrew Flintoff will undergo ankle surgery early next week and is expected to be out for 12 weeks.
The diagnosis means he will miss the rest of the Pakistan series and faces a race against time for the Ashes.
Flintoff had thought rest and rehabilitation would solve the problem with bone fragments in the left ankle.
But he experienced discomfort bowling on the final day of Lancashire's match against Kent, supposed to be a final fitness check before his return.
"If the predictions for the rehabilitation and recovery are on course he will be fit before we set off for Australia"
Andrew Strauss will again lead the side in next week's second Test at Old Trafford, with first Test centurion Ian Bell likely to keep his spot when the squad is named on Sunday.
"Andrew Flintoff saw a specialist on Saturday morning where it was decided that further surgery is required on his left ankle," said a statement from the ECB medical team.
"His rehabilitation and return to full fitness is anticipated to be in the region of 12 weeks."
England open their one-day ICC Champions Trophy campaign in India in exactly 12 weeks' time, with the Ashes beginning in Australia on 23 November.
The county season ends on 24 September, making it difficult for Flintoff to have any meaningful match practice before an arduous international winter.
Nevertheless, chairman of selectors David Graveney is holding out hope Flintoff will be back in time to face Australia.
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"He has worked really hard for the last four or five weeks to get to this point," said Graveney.
"I don't think I've ever seen him as fit as he looks at the moment, apart from his ankle.
"But if the predictions for the rehabilitation and recovery are on course he will be fit before we set off for Australia."
Flintoff is the third player from England's successful Ashes side to undergo surgery after initial medical advice that rest would be sufficient.
Captain Michael Vaughan has already been ruled out of the Ashes to have an operation on his right knee.
Spinner Ashley Giles hopes to return in time to face Australia after a second hip operation but has not played since last November.
A fourth Ashes hero, bowler Simon Jones, is a major doubt for the rematch in Australia after a string of knee and ankle problems.