Cook revealed that he did not recognise the culture of bullying Pietersen has alleged occurred in the dressing room and said that he feels hurt by the claims in the book, published on Thursday.
Cook said that he thinks it has been a really sad week for cricket, adding that they have to draw a line under it at some stage and this is a good time, The BBC reported.
Cook and Pietersen last played together in January when England were whitewashed 5-0 in an Ashes series against Australia. The pair had previously featured in a side which reached number one in the world rankings in 2011 under former captain Andrew Strauss, and were also members of Ashes series wins in 2009, 2010-11 and 2013.
Cook said that he is very proud of that era, adding that he really only has fond memories of that. But, he said that he does believe it has kind of been tarnished and he is sad about that.
Pietersen's England career was effectively ended in February when his central contract with the England and Wales Cricket Board (ECB) was terminated. He scored 8,181 runs at an average of 47 in 104 Tests and captained England in three Tests.
In response to the book's claims of bullying within the England dressing room, Cook said that international cricket is a tough place and, as a team, one is striving for excellence at all times.
Cook said that certainly at some stages those frustrations boiled over more than they should have done, but added that that was only people who were desperate to succeed and wanting to know the other 10 blokes around them were committed 100 percent to it also.