The injury-plagued Flintoff also looks likely to miss the tour of New Zealand in February and March next year as selectors try to get one of their prized-assets fit for the home series against the Kiwis and South Africa next summer.
"The ECB medical team have announced that Andrew Flintoff underwent keyhole surgery on his left ankle at a hospital in Holland on Friday," said an ECB statement.
"He will now undergo a period of rest and convalescence followed by a rehabilitation programme.
"It is anticipated that Flintoff will be able to resume full training in the New Year and following discussions between the ECB Medical team, the England selectors and Flintoff, it has been decided that the priority will be for him to regain full fitness ahead of England's home international programme in 2008.
"Flintoff will not be made available for this winter's Test series in Sri Lanka and at this stage it is considered unlikely that he will participate in the tour of New Zealand."
Flintoff missed the home Test series against India and the West Indies as a result of injury although he did return last month for the ODI series against India in which his tight bowling played a key role in an eventual victory.
The 29-year-old has missed 11 of England's last 16 Tests as well as 21 of their last 48 ODIs.