Knee problems kept Pietersen out of action for three months earlier this year and the 33-year-old's recurring injury has now flared up again just weeks before the Ashes gets underway Down Under.
Despite Pietersen's injury setback, Flower remains hopeful that the player will be able to face Australia in the first Test in Brisbane.
Flower told reporters: "Kevin has had a slight recurrence of that knee issue, and he'll be going to Melbourne for a scan and a cortisone injection, so he won't be travelling with the rest of the team [to Sydney for next week's four-day match against a New South Wales XI].
"I don't think it's going to be a huge issue. He's had a couple of these injections before, and they've been successful.
"They've quietened the problem down, and it's obviously an ongoing issue for him. We anticipate this one being successful and him playing a full part in the Ashes tour."
The first Test is due to begin on November 21.