The Australian international has not played since last December although he was expected to be back in the side before now.
"Danny will visit a specialist in London on Friday and it is looking very unlikely that he will play again this season," Keegan told City's official website. "It is nothing major but we just need to find out what is causing this. He has worked hard and got himself back ready to train with us. "He went in with the physio the day before he was due to join in the squad session but did not get through it." "There is obviously something there that he is not happy with so we will find out more when he returns from London. It looks doubtful that he will be fit again this season."