The 30-year-old Republic of Ireland international had to be substituted during the 4-0 win at Crystal Palace after suffering a recurrence of a hip problem.
Blues manager Lee Clark told the Birmingham Mail: "Keith has got a recurrence of a hip problem that kept him out of the Ireland squad in the Euros.
"That's affected his groin area as well. We got really concerned as he had a lot of bleeding in his groin area which came out in a bruise.
"When we had it scanned, the hip area was the problem.
"So he is certainly out the six remaining games and we need to know where we are further down the line so he needs to see a specialist."
Fahey returned to action for Birmingham at the end of September after missing Euro 2012 but he was then granted compassionate leave in October for personal reasons.
He made his comeback as an early substitute in the 1-0 home defeat to Middlesbrough on March 16 before suffering his latest setback on his next appearance.