The South Africa-born batsman, axed by England earlier this year after the team's 5-0 Ashes thrashing in Australia, claimed there had been a "bullying" culture under Flower, but saved his most stinging criticism for Prior, whom he accused of being a "bad influence".
Pietersen made the accusations in an explosive interview with a British newspaper which was published on Monday ahead of the release of his autobiography on Thursday.
He claimed Prior was the ringleader of a group including senior bowlers Graeme Swann, now retired, Stuart Broad and Jimmy Anderson, who would lay into their team-mates for dropping catches.
Former England captain Hussain said he had some sympathy for Pietersen's views.

"It really tells you a lot about team spirit ... always there when you're winning but always fades away when you're losing,” he said.

"A lot of the stuff I've read (from Kevin) this afternoon, I've nodded at and agreed with ... about shouting at players in the outfield. Team spirit is about respect … what happened in the end was that the respect had gone,
between Kevin and his team-mates,” he added.

"Once you lose that respect, and then start losing games of cricket, I'm afraid the wheels can only come off," added Hussain, who played his last Test in 2004 - the year before Pietersen made his Test debut.
Pietersen insisted he had not given up hope of playing for England again but Hussain said he could not see how a return was possible, given Pietersen's outspoken comments about the England and Wales Cricket Board (ECB) and lack of recent form.
"Some of the stuff he writes in this book, I can't see any way back for him," Hussain said.

"The best way to answer his critics, and pile the pressure on (England captain Alastair) Cook and the ECB was to go out there and smash hundreds for Surrey ... he never did that, and is letting his book do the talking instead of his batting,” he added.

Former England off-spinner Swann led the angry responses from the targets of Pietersen's ire.
Swann, who retired midway through the last Ashes series, made it clear that he was unimpressed by Pietersen's version of events.
"I expected it to be the biggest work of fiction since Jules Verne and that seems to have happened. The one thing I will say I immediately realised it was codswallop when I read the character assassination of Matt Prior," Swann was quoted as saying.
"Tragically I don't think Kev realises the one person who fought tooth and nail to keep him in the side is the one person he is now assassinating: Matt Prior,” he added.
Prior, currently sidelined through injury, responded to Pietersen's comments by tweeting: "Obvs (obviously) sad to see the accusations against me this am (morning) and I WILL have my right of reply! However today is not the day and Twitter is not the place for it!”
"Now back to my Achilles rehab and learning to walk again! have a great day everyone,” he added.
Chris Tremlett, who was part of the squad that was whitewashed by Australia, was more supportive and tweeted: "Glad Kevin has finally been able to give his side of the story.”
"People can now make an informed opinion of what went on
in the dressing room,” he added.
The England and Wales Cricket Board (ECB) said it was "impossible" for it to comment on Pietersen's claims as they hadn't yet seen the book.
But former England national selector Geoff Miller, speaking at an ECB function at Lord's on Monday, said: "To my knowledge, there was no atmosphere of bullying within the England set up.”
"What we as a selection group tried to do was to pick the best squad to create the best atmosphere to win matches,” he added.

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