In the wake of the 5-0 Ashes whitewash Flower said he was not willing to discuss the futures of individual players and that was followed by a report in the Guardian, also run in various other UK national newspapers, that his relationship with Pietersen had fallen apart.
"Following speculation in the media today I feel it necessary to reiterate much of what I said in my recent press conference," Flower said. "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."
Earlier, Pietersen had taken to Twitter to make public his desire to play the next Ashes in 2015. "Very disappointed to lose 5-0, and not to score more runs personally. Tough tour against a top class team." Pietersen posted. "I want to thank all the England fans for their terrific support. And I'm determined to help regain the Ashes in 2015."
But that decision ultimately rests with Flower, England's team director, and perhaps the captain, Alastair Cook. Flower's mood has probably not been lightened by a suggestion from Michael Vaughan, a former England captain, that Pietersen should become vice-captain deliberately to break down a culture of "yes men" that has grown up around the England set-up.
Vaughan has since expressed the fear that Pietersen could become the scapegoat for England's Ashes defeat . "I hope England do not take the easy way out of this mess by making Kevin Pietersen the victim for the Ashes whitewash," he wrote.
Flower has wasted no time in indicating to the new managing director of England cricket, Paul Downton, that he wants full authority to rebuild England's Test side as he sees fit, with the final say on selection.
What remains unclear is how much that would impact upon Pietersen if such power was granted. In comments immediately after the series, Flower merely remarked: "There are always some personal agendas in most teams. No team is perfect and our team is no different. Team spirit always gets its closest examination under pressure and we have been put under a tremendous amount of pressure by a good side on their home turf. That is one area we will look at."
But Flower's mistrust of Pietersen is rarely far from the surface and he may see this as an opportunity to build a new young side without what he might regard as rebellious influences.
Mike Selvey, in the Guardian, has no doubt about naming the culprit, real or imaginary: "So adamant is Flower that the presence of Pietersen in the dressing room is detrimental to the future development of the side that he is believed to be prepared to resign his position should Downton, James Whitaker, the new national selector, and Cook - if he retains the captaincy - insist that Pietersen should be a part of that process."
He refers to Flower's relationship with Pietersen since the long-running furore in 2012 as nothing better than "an uneasy truce" and claims: "On this tour, despite his assurances before his 100th Test in Brisbane that he was committed to England to 2015 and beyond, it is thought that Pietersen's influence in the dressing room has been divisive."
Part of the debate around Pietersen's future stems from his fitness; he needed an injection in his knee before the Ashes began having been forced home from the tour of New Zealand in March and then did not play again until shortly before the Ashes in England.
His workload is being carefully managed by the ECB, including being rested from the one-day series against Australia which starts in Melbourne on Sunday. It remains to be seen whether he will play on the short tour of West Indies which starts at the end of February although would be expected to feature at the World Twenty20, despite only playing once for England in that format for almost two years.
The man himself has always insisted he wants to be part of England's attempt to regain the Ashes in 2015. He has also spoken about a target of 10,000 Test runs - he currently stands on 8181 after a disappointing return of 294 runs at 29.40 in Australia, although that still made him England's leading run-scorer.
Pietersen's involvement in IPL, however, will add to the tension, amid speculation that players will have to sign three-year contracts and be available throughout the tournament. Neither undertaking has yet been demanded by the franchises and, if it was made, the reverberations would stretch much further than Kevin Pietersen.
*January 7, 15.30 GMT: This article was updated with new material
David Hopps is the UK editor of ESPNcricinfo