Yet another dismal collapse saw England bowled out for 166 in their second innings of the final Test to confirm a 281-run win for Australia and a 5-0 whitewash for the tourists.
England's batting has in particular been a cause for concern, with only one century scored during the series - compared to 10 from Australia - and a highest first-innings total of 255.
And Flower admits their confidence has taken a big hit.
"We've underperformed badly," he told Sky Sports 2. "If I'm honest, we could have seen it coming a little earlier.
"We've underperformed in the first innings for quite a long period of time. We haven't scored many runs, haven't scored any first innings above 400 for a long time, and people lost confidence early on in this tour.
"The pace rocked the batting order in the first Test and we never quite recovered.
"I would like to pay tribute to the Australia camp. Their bowling attack has been outstanding.
"We've seen a sustained style of bowling, exceptional pressure and (Mitchell) Johnson's pace has been a huge difference between the two sides."
Even before the final Test, questions had already been asked over the future of England captain Alastair Cook and many of his players, as well as Flower's own position at the helm.
The coach is aware there is a need to dissect the tour in detail, but does not think this is the right time to be making rash decisions and would prefer a period of reflection first.
He said: "I as leader, along with Alastair, we have to examine the things we've done, the decisions we've made, the influences we've had and they obviously haven't been good enough.
"But I think a full and logical review at some stage in the near future might answer some of those questions.
"This does feel like the end of an era of some description. It is a chance for some sort of renewal for the England national cricket team, we'll look at how that renewal pans out.
"We certainly weren't good enough, so there should be change of some description. It needs wise people making good decisions at the top to try and get those decisions as right as possible.
"But we should take a bit of time to review it properly. It would be remiss of me to stand here and start making crazy predictions or to decide anything without consulting those who need to be consulted."
Flower also feels it is wrong to be singling out Cook - or any other player - for personal criticism on a tour in which very little has gone right for the squad as a whole.
"No team is perfect and ours is no different," he said.
"Team spirit always gets its closest examination under pressure and we've been under enormous amounts of pressure by a good side on their own turf. That is an area we will look at.
"All cricket captains need an authority and need to lead and the team needs to be led and need a leader to do that.
"Alastair is a good man, has done some amazing things for his country already in a sporting context and will do more of that in the future."
The humiliating whitewash appears to have done little to dampen Flower's own enthusiasm for the job either.
He said: "I still enjoy it, still find it fascinating. It's a great job and I'm very proud to be associated with England cricket."
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