Inverness have announced an annual deficit of £378,487 in the year to 31 May, 2012.
Caley finished 10th in the SPL last season after making a poor start due to a series of injuries and it is the cost of covering these absences that has led to the loss, according to chairman Kenny Cameron.
The likes of Aaron Doran, Chris Hogg, Owain Tudur Jones and Jonny Hayes were all hit by long-term injuries.
Cameron said: "Every club has injuries but this extensive sequence of casualties, and their severe nature, was unprecedented in the club's history.
"It triggered physio and medical expenses significantly beyond budget and left us with no alternative, if we were to stay in the top flight, but to increase the playing squad considerably beyond the financial target which had been set.
"This scenario contributed to the majority of the losses incurred in the year under review. However, my view is that had we not taken the decisions we did, the outcome may well have been even more financially devastating for the club."