Several national newspapers reported that Flower was willing to walk away from his job if Pietersen remained in the long-term plans of the England and Wales Cricket Board (ECB).
Flower and Pietersen have endured flashpoints before, most notably in the 2012 summer when Pietersen was left out of the England team after his texting controversy and abrupt decision to retire from one-day internationals.
But claims that Flower is now ready to move forward without Pietersen – after the 45-year-old coach was given ECB backing to retain his job in the wake of the Ashes debacle – were quickly dismissed.
Flower described suggestions he had issued an ultimatum as “totally inaccurate” in a press release issued by the ECB.
Flower added any decisions would not be made so soon after an emotionally taxing series.
“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.”
Pietersen too felt the need to comment on the newspaper reports, via Twitter, saying “I am shocked and saddened by reports in the media today concerning my future with England.
“I wish to repeat my strong desire to continue playing for my country, and to help us regain the Ashes in 2015,” added Pietersen.