Pietersen was keen to retire from 50-over cricket and continue playing Twenty20 internationals, but the ECB would only allow him to play in both forms of the game or neither.
Consequently, Pietersen will not be available for the upcoming one-day series against Australia, and Warne said in The Independent: "It staggers me and I'm very surprised that the ECB didn't try and negotiate that better, drop their egos and say, okay we understand this, we want to keep our best players playing all the time."
He added: "Any team that hasn't got Kevin Pietersen is significantly weaker. He's a match-winner so that's a big loss.
"I think it's just a bit too much ego for my liking from the ECB.
"Who wouldn't want Kevin Pietersen in your side? He's a match-winner and he puts bums on seats because people love watching him play.
"He rubs off on the rest of the players. So to me it's a huge loss.
"People might give up more one-day cricket or they might give up Twenty20.
"Michael Clarke's given up Twenty20 in Australia because he can't play all three forms at that level, but you can't imagine Australia dropping him and saying don't worry about one-day cricket, just stick to Tests."