Flower publicly pledged to stay on and rebuild the team following England's humiliating 5-0 Ashes defeat.
The Guardian's cricket correspondent Mike Selvey claims that behind the scenes the Zimbabwean's future is anything but certain - and at the heart of the issue is his relationship with England's star batsman, Pietersen.
"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," Selvey wrote in his report.
Both Flower and skipper Alastair Cook have been given the backing of the England and Wales Cricket Board, and England Cricket's newly-installed managing director Paul Downton is also thought to be right behind the pair.
Pietersen was England's top scorer during the Ashes - albeit averaging less than 30 - but his issues with Flower go back to the summer of 2012, when the South African-born batsman sent text messages to members of the touring South African party that were scathing about then-captain Andrew Strauss.
The 33-year-old returned to the team a few months later and was one of the star performers during the famous series win in India - and he stated after the Sydney Test that he wants to stay on in the side until at least the 2015 Ashes.
But Selvey claims that Pietersen and Flower's relationship has been one of "uneasy truce" for 18 months, and that fresh wounds were opened Down Under by Pietersen's string of rash dismissals at the exact moments when England needed to dig in.
"As a senior player, the nature of a number of his dismissals when apparently batting comfortably has led to some strong exchanges," Selvey continues.
"Flower is thought to believe that the future development of the team can only happen without Pietersen."