Pietersen is making slow progress following the Achilles surgery he had after the second Test against Australia and his recovery has been hampered by an infection.

England name their squad for the South Africa trip after the Champions Trophy with the one-day series starting in November followed by the Tests either side of Christmas.

There had already been concerns that Pietersen was struggling to make the one-day series and Flower isn’t sure of his participation.

“We’re still taking that day by day. We’re still not sure whether he’s going to be fit or not,” Flower told reporters.

“The infection that he got initially and the subsequent lack of healing that’s taken place since then has set back his recovery. He had quite a horrible wound after the infection took hold.

“I’m not sure exactly of what he’s able to do at the moment; the medical people have been handling that. I would have wanted him back at the start of this one-day tournament.”

Jonathan Trott’s debut century against Australia ensured Pietersen’s loss for the final three Ashes Tests wasn’t terminal, but the one-day side has struggled hugely in his absence. Without Pietersen, who has scored two of the three ODI hundreds England have managed since the start of 2008, the middle order lacked any presence against Australia.

While Pietersen may yet recover in time for the tour of his homeland, one man who won’t be there in any capacity is Andrew Flintoff.

He was already ruled out following his knee surgery and last week he turned down the offer of an incremental contract from the ECB, so he can take up a series of lucrative Twenty20 and TV opportunities, but Flower said he wasn’t too shocked at Flintoff’s decision.

“I wasn’t overly surprised he turned down his incremental contract because it is not a lot of money,” he said. “I haven’t chatted to him just recently, but let’s wait and see how fit he gets and when he comes back first.

“Fred (Flintoff) has made himself available for one-day international and Twenty20 cricket.

So I’ll take him on his word that he’s going to be available. As far as I understand it he wants to play for England again in one-day internationals and Twenty20 cricket and I look forward to having him back and I’m sure he’ll be fully committed when he comes back. (Cricinfo)