The former Liverpool striker has not starred for City since storming away from the ground after being substituted in the 1-0 defeat by Everton, but Keegan insists their is no rift between the two.
"I had a chat with Robbie a week ago and we decided to spend until after the international break getting him as fit as we possibly can," said Keegan.
"There has been no bust-up. When I sat down to talk to my players afterwards, he wasn't there and that is not right.
"I asked him to give me a good excuse and he couldn't. I understand his frustration and he is not the first player to do it but he accepted he was wrong and I fined him."
The City boss added: "I promise Manchester City fans the next time they see Robbie Fowler, it will be a different Robbie Fowler.
"As hard as he has tried since he came here, Robbie knows his level of fitness is below what he really needs to have.
"He looks in better shape already but he has to go beyond that now. He has bought into the situation big-time and we have worked together this week but he knows there is no quick fix."