The Durham seamer, who has a history of back trouble, was left out of the three-day match with South Australia match as a precaution after waking up with tightness in his side.
Harmison, who has a history of back trouble, was left out of the side for England's three-day match with South Australia match after waking up with tightness in his side.
He missed the one-day series against Pakistan in the summer with a lower back injury (which could bring side pain) but returned for the ICC Champions Trophy.
"It's similar to the one he had during the summer, which just irritated him, although he could bowl," said Fletcher.
Flintoff added after close of play on day two in Adelaide: "He's run in, he's bowled and injuries for fast bowlers are part and parcel of the job.
"He's had a scan, which was pretty inconclusive. They have given him an injection and he says it has improved," said Fletcher.
"We just have to see what happens on Sunday morning, how he pulls up.
Harmison missed the one-day series against Pakistan in the summer with an injury described as being to his lower back (which could bring side pain) but returned for the ICC Champions Trophy.
"He's a key player for England - he has been for a long time now in the Test side - and we want him fit."
Lancashire seamer Sajid Mahmood replaced Harmison for the warm-up game and went wicket-less on day one.
But the England coach was impessed by the performance of England's three senior seamers, who shared five wickets.
Matthew Hoggard took three wickets in 12 balls and James Anderson shared the new ball with him, dismissing former Test batsman Matthew Elliott.
"The morning session was as good as I've seen England bowl for some time - there was good discipline, good control and they didn't lose their concentration," Fletcher added.