Television personality Piers Morgan is close friends with Kevin Pietersen, who saw his international career come to an end on Tuesday when the ECB informed him that he was no longer part of England's plans.
Morgan claimed on his Twitter account that Prior told teammates Flower was creating a "schoolboy environment" after being dropped for the fourth Test in Melbourne.
"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," Prior posted on his own Twitter account.
"I'm not the kind of person to divulge what is said in team meetings but all I will say is that Flower, Cook and the rest of my teammates know exactly what I said and the way in which it was meant!"
Flower resigned from his role as team director last week.