Both defenders were dropped following the 5-0 drubbing by Arsenal and Keegan felt the side were more solid defensively in the defeat at Blackburn last weekend.
"I thought defensively we looked much better," the City boss told BBC GMR.
"I have been very loyal to Steve Howey. He has played nearly every game since I have been here.
"I am going to look at other options now in his position, in Richard Dunne's position and maybe one or two other positions.
"I wouldn't be doing my job properly if I didn't do that."