The Cumbrians, who released their statement ahead of the club's annual general meeting, also confirmed turnover was down £652,141.
A club statement read: "Excluding depreciation and amortisation, the company had an operating loss of £124,329 with some key areas of movement.
"The turnover was down £652,141 - all of which was attributable to less football income (Johnstone's Paint Trophy/Football League Trophy income was reduced by £420k, player sales reduced by £105k and FA Cup income reduced by £41k).
"In terms of expenses, player basic wages were reduced compared to 2011, although bonus payments for league position were higher, and in return we did not achieve a play-off position or increased crowds."
The club is hoping to realise savings of £230,000 in running costs by the end of the 2012/13 financial year.