Some newspapers claimed late on Tuesday night that Flower was ready to walk out on England if Pietersen was retained beyond this winter's disastrous Ashes tour of Australia.
Flower has described the reports of an ultimatum, in a statement issued by the England and Wales Cricket Board shortly after the allegations surfaced, as "totally inaccurate".
Following the 5-0 whitewash Flower publicly stated his desire to remain in his post and build a new era for the Test side.
And he has insisted suggestions he is prepared to do that only without Pietersen - who has himself stated a desire to stay on and try to regain the the urn in 2015 - are unfounded.
"Following speculation in the media today I feel it necessary to reiterate much of what I said in my recent press conference," Flower said in the statement.
"It would be sensible and responsible to review the tour in a calm and logical manner before assessing our options for the future and planning ahead.
"I repeat that neither I nor the wider ECB leadership group have made any decisions as to the future involvement of any individuals in the playing group or in the support staff.
"The reports that I have issued an ultimatum of some description to the ECB are totally inaccurate."