England crashed to a 5-0 Ashes series whitewash to the Australians, the first such defeat in 86 years.
Fletcher, also under fire for his part in the tour debacle, conceded he was concerned before the series that Flintoff would be over-burdened by the captaincy on top of batting at No.6 and opening the bowling.
Fletcher also said Flintoff had difficulties deciding when to attack or defend in the field, and had lacked the equivalent support that Australian skipper Ricky Ponting could so often call upon.
England are expected to replace Flintoff with Michael Vaughan on Sunday for next week's triangular One-day series against Australia and New Zealand.
Vaughan's knee problems prevented him from playing in the Ashes series, but he is available for the tri-series.
Flintoff struggled with both bat, averaging 28.22, and ball (43.72) through the series, and had his tactical ability questioned after setting defensive fields against Australia's batsmen.
Fletcher said he wondered before the series whether appointing Flintoff to replace Vaughan over opener Andrew Strauss was the right call, given the Lancastrian had only captained England in six Tests beforehand and did not lead his county.
"I do believe there is a lot to ask of him, especially with a young, inexperienced side where you've got to do a lot of captaining," Fletcher told reporters here Saturday.
"You're not really getting the help from these young guys that, say, Ponting gets from the experienced guys around him. So it is a very difficult job for him.
"He found it difficult. With a lot of young bowlers out there he's got to (decide whether to) protect them, or does he go and attack a side of attacking batters?
"He's come up with a policy that he believes is right and it's been a very, very difficult job for him."
Flintoff's difficulties even extended to managing his friend and strike bowler Steve Harmison, who failed to reproduce his form of England's 2005 Ashes victory in England.
Harmison took 10 wickets at 61.40 and only bowled his best when the Ashes were lost.
"There were a couple of occasions during this (fifth) and other Tests when Andrew has taken him (Harmison) off and he has been pretty angry about it," Fletcher said.
The review of England's dire tour will include its limited preparation before the first Test, its bad selections, Fletcher's role as a selector, Flintoff's captaincy and even the size of the team's entourage.
"We can go away and there's areas we can work on. We've said it on numerous occasions, cricket's not an easy game, you have your ups and downs," Fletcher said.
"If it was just that simple to get players to play well. There was a lot of pressure. You've got to give credit to the Australians, the way they played, they're a quality side.
"Last (time, in 2005) they had their downs with the same side. They've come back, turned it around and beat us convincingly. We hope to do the same."
England have won just five of 18 Tests since regaining the Ashes in 2005, but Fletcher said there were enough positives to warrant a No.2 Test ranking.
Fletcher also maintained he was the right man to coach England and said he would discuss his recommendations for the future in the review.