All-rounder Flintoff, 27, played a key role in England's 2-1 Test series win in South Africa but has flown home before the one-day leg of the tour to have an operation on a longstanding ankle injury and give himself enough time to recover for the visit of Ricky Ponting's world champions.
Despite England having acknowledged the dangers of over-bowling Flintoff, the Lancashire paceman was again given a heavy workload despite being troubled by a bone spur problem.
And he told Sky Sports Thursday: "I had an injection last week to get me through the (fifth) Test match but I've got time now to get it (the operation) done.
"I've got a few weeks to get fit for the start of the season. I've had a few injections over my career, but this is a different sort of injury."
Flintoff, also a hard-hitting batsman, tried to downplay the impact all his bowling had had on his injury.
"The workload has played a part but lots of bowlers have had this done. It is just a case of getting this window of opportunity. It has come to the point where I need to get it done and there was no other time."
Flintoff has still to play a Test against Australia despite making 45 Test appearances and didn't feature in the last Ashes series, in 2002-03, because of a hernia problem.
England have a two-Test series at home to Bnagladesh starting on May 26 before they are involved in a triangular one-day competition with the Asian minnows and Australia.
They then play four separate limited overs internationals against Australia before the first Ashes Test starts at Lord's on July 21.