"I think there's been an ongoing dispute between Kevin and the England management for quite some time," Fraser told BBC Radio Five Live.
"Kevin contributes to the team with the runs that he scores but the fact that all this sort of stuff is going on has been a major distraction to the team.
"England pick the group of players that they believe have got the best chance of winning the game. I think the ECB have made the right decision by leaving Kevin out of this game."
Pietersen announced at the weekend that he has gone back on his original decision to retire from limited-overs cricket by insisting that he wants to play all forms of the game with England.