Cook said there had been occasions when players overstepped the mark.
"International cricket is a tough place and as a team you are striving for excellence at all times," he said. "Certainly at some stages those frustrations probably boiled over more than they should have done. But that was only people desperate to succeed and wanting to know the other 10 blokes around them were committed 100 per cent to them.
"Did it over step the mark a couple of times? Possibly, but we addressed those issues - this is something that always happens in teams. It certainly wasn't a 'bullying environment' at all in my eyes."
Pietersen claimed Flower had allowed the "bullying" culture to develop and described him as "contagiously sour".
Pietersen's criticisms of Prior, who he described as "back-stabbing", came as a huge surprise to Cook. "That was probably the biggest shock for me," said Cook.
"He is a great man who has been a fantastic servant for English cricket."
- The Independent