Flower is confident cricket will survive the scandal
Kevin Pietersen will face disciplinary action over the Twitter tirade in which he accidentally announced his dropping from the England team.
Pietersen pre-empted the official squad announcement when he told followers of his feed about his omission.
England coach Andy Flower said: "He says he made a bit of a mistake, and I'll take him at his word.
"But still there'll be a disciplinary hearing because we can't have situations like that happening."
Pietersen used an obscenity to describe the decision to omit him from England's NatWest Twenty20 and one-day international squads to face Pakistan.
Flower said he has accepted the out-of-form batsman's explanation that it was an honest mistake.
Pietersen thought he was 'texting' a small number of friends when in fact he was announcing his omission to the world.
It's a great, great game, people love playing it and people love watching it and that's why it will survive
England coach Andy Flower
Former England Under-19s captain Azeem Rafiq received a one-month ban earlier this summer over a similarly foul-mouthed Tweet.
"I didn't connect it at all with that," said Flower, when invited to compare the two cases. "But yes, it is important to be consistent.
"We want to allow the players to use that form of the media, if that's what they choose to... but with that freedom comes responsibility."
Flower also explained that his decision to drop Pietersen was "of course, a difficult call".
"When you're making decisions about people's careers and their lives it always is difficult - and you've got to do it responsibly.
"The intent, and reasons behind that non-selection, are very simple.
"In one-day internationals, Kevin has under-performed recently - over the last 12 to 24 months.
"He acknowledges that - and with regard to the Twenty20s, there is a four-day game starting at The Oval on the day that the second Twenty20 is played.
"In our opinion, it would be more important for Kevin to play that four-day game and then the following one - rather than being involved in limited-overs cricket - with the priority being getting him into form and confidence for the Ashes."
Meanwhile, Flower has urged his side to focus on the imminent limited-overs series and not be distracted by the scandal engulfing Pakistan.
Test captain Salman Butt and bowlers Mohammad Asif and Mohammad Amir have been accused of corruption and are being questioned by police.
England face the tourists in the first of two Twenty20 matches on Sunday.
"No-one wants that sort of news on the front or back page but we have to focus on playing the game," said Flower.
"We have a T20 game on Sunday [in Cardiff] which we are working towards and we want to keep it as simple as that.
"We don't want to live in a world of 'what ifs' and we are looking forward to the game on Sunday."
However, Flower did admit that the allegations and the publicity they have generated have done little for the image of the game.
"We have to see the outcome of these investigations first but obviously it's not a very healthy position we seem to find ourselves in right now," said Flower, whose side will also play five 50-over internationals against Pakistan.
"But the game will survive, it's a great, great game, people love playing it and people love watching it and that's why it will survive."