Speaking after England's historic win over Australia at Lord's, Flower also revealed that an injured Pietersen had not yet ruled himself out of the series.
"No, that's not the case at all, definitely not. It's a medical decision that's got to be made. Kev is seeing a specialist later this week and they'll assess his achilles problem. We just get the expert advice and take it from there," The Guardian quoted Flower, as saying.
"Fred obviously had a tough physical game but chatting to him [yesterday afternoon] he was very bullish about being ready for the third Test. Obviously with his injury record we've got to be a little bit careful about the wear and tear on his body but he can have a proper rest over the next week and he will also be reassessed," Flower added.
Asked whether England could beat Australia for only the second time since 1986-87 if Pietersen and Flintoff were unavailable, Flower said: "Definitely. When asked before the series whether we believed we could win the series, I said yes. Whether we will or not we don't know. We're going to have to play very good cricket."
Flower, who will help pick the third Test squad, to be announced on Sunday, did his best to play down the seriousness of Flintoff's potential absence.
"If he's out of the side, of course that's a blow. But we've got a few fast bowlers waiting in the wings who can be successful in international cricket. Obviously we want Flintoff in our side but we will see if his body's up to it. If not, there are other guys who can do a good job. He knows what a significant contribution his was. With him leading the attack in the last innings, that gave us belief we'd bowl them out," Flower said.