Pietersen was left out of the third and final Test against South Africa on Sunday after allegedly sending a number of derogatory texts about his teammates.
Flintoff, one of his former playing colleagues, has warned the ECB against permanently leaving Pietersen out of the squad.
"If England do want to dominate you need your best players, and Kevin Pietersen is definitely our best player. Hopefully they can salvage something and get him back in the team," Flintoff told talkSPORT.
"Any team without KP is a weaker team. You've seen what he's done with Test cricket, one-dayers and Twenty20 for England, so it is a detriment to the side.
"If England are to be the number one side in the world, he has to be in it. We will see what happens but measures should be made within the dressing room."
Pietersen has been replaced in the England Test squad by Jonny Bairstow.