Pietersen was named man of the match in the drawn second Test against South Africa after an imperious century and career-best bowling figures, but refused to confirm that he would continue playing international cricket past the third Test.
Pietersen has already retired from England's ODI and Twenty20 sides, and Flintoff believes that the two parties need to come to a solution in order to keep the batsman involved in the set-up.
"I suppose it's up to the ECB and Kevin to sort it out. They need to get in a room, sort it out and move on because I imagine Andy Flower and his team want it resolved," Flintoff told Sky Sports News.
"Any side with Kevin Pietersen in it is a better side, whether that's the one-day side, Twenty20 or the Test side."
England must win their third Test against South Africa in order to avoid being replaced by the Proteas at the top of the Test rankings.