"Flower's behaving like a headmaster, this is a schoolboy environment. F**K Flower! This is OUR team!' - @MattPrior13 to England team," Morgan tweeted.
Morgan also said Pietersen was popular with the younger members of the team. He described Prior as a hypocrite for siding with the players who were upset at Flower's methods, but then stabbing Pietersen in the back when talking to Flower, who quit last week, about the issue.
The accusations were denied by Prior, who was dropped for the final two tests in Australia after a run of poor form.
"I don't do this PR, spinning media rubbish," Prior said on Twitter.
"But I refuse to be attacked by a bloke that knows very little about what goes on in the England setup apart from rumour, gossip and hearsay from certain individuals (most of whom I'd take with a pinch of salt!!).
"Maybe I was recorded or 'hacked' but if not I'd like to see where these words I apparently said have come from? There is no story here just an attempt to knock someone who has only ever had the team's best interests at heart."
The Daily Telegraph reported that a team meeting in Melbourne on December 30 brought about the end of Pietersen's international career this week after 104 test matches, 136 one-day internationals and 37 Twenty20 internationals.
The paper said a players-only meeting was held in which they agreed that the team were relying too heavily on Flower to provide instruction.
Pietersen then allegedly went on an anti-Flower rant, but missed the point of his team mates' concerns, believing they were accusing Flower of being overly "prescriptive" rather than "paternalistic", the Telegraph reported.
Flower heard about the meeting and wanted an explanation from Pietersen. He then asked the players if they had a problem with his methods, which they said they did not.
The issue was discussed with Paul Downton, the new managing director of England cricket, who after meeting Flower, coaching staff, captain Alastair Cook and other senior players, decided to end Pietersen's international career.
(Reporting By Josh Reich, editing by Ed Osmond)
