Lower figures for gate receipts, and media and commercial income, contributed to the losses along with a higher wage bill and "other expenses" of £800,000.
Ipswich made £10.8m on player transfers in the year ending June 2011 following the sales of Connor Wickham and Jon Walters, but that figure plummeted to just £248,000 over the next 12 months.
The overall turnover was down by over £2m to £15.04m, while the club's overall debt rose to £79.62m.
Club officials have set their sights on reducing the wage bill to prepare for the implementation of the Financial Fair Play regulations.
Ipswich's wages-to-turnover ratio is one of the highest in the Championship at 119% - an increase of 17% on the previous year.
The accounts also revealed that former Town chief executive Simon Clegg earned an annual salary of £193,000.