A 58th minute strike from Spanish midfielder David Lopez saw the Seagulls climb to sixth, but Crofts had to be helped off shortly before the finish and Garcia is worried the injury could be a serious one.
He said: "I'm not 100 per cent sure, but the injury could be a bad one. We won't know until he has a scan and we see the result.
"It's the worst news of the day and sad for Crofty because he's been having a terrific season."
Garcia played down Albion's elevation to the top six by insisting he was no happier than when his men had won previous games.
He said: "I prefer to see the performance of the team. Some games we played well yet didn't win. We have to keep going and at the end of the season we'll see where we are."
Brighton clinched victory without midfielder Liam Bridcutt, reportedly a target for former boss Gus Poyet at Sunderland, but Garcia stressed he missed the game due to a groin injury.
The Spaniard added: "He's not 100 per cent and we need people 100 per cent to play. If he is fit enough I will play him. We want to keep him because he is one of our main players."
The single goal defeat ended Birmingham's 10-match unbeaten run and, apart from complaining at a lack of quality in the final third of the field, manager Lee Clark was delighted with the effort of his depleted squad.
He said: "We were exceptional under the circumstances. We've a depleted squad and had lost five players from the starting 11 since Boxing Day.
"We got into some great situations, but our final ball was not to the required or usual standard. It's frustrating for the players because they've given me absolutely everything again.
"But we have to go again and go on another unbeaten run. The level of performance in terms of effort and application was there again. I can't complain about what the players have given."
Clark is relishing the challenge of producing a competitive team while balancing the books, and was delighted with the way teenager Reece Brown responded after coming off the bench.
He admitted: "It's getting harder because I'm losing players but Reece came to the fore today."
Clark also explained three loan players had been recalled to their clubs, decreasing the size of his injury-hit squad.
"The young players have been brilliant for me. I hope to add one or two to the group as well as having players come back from injury. We've lost Dan Burn, Jesse Lingard and Aaron McLean to their parent clubs and that's been a blow to us."