Whitehall auditors have refused to sign off the Treasury's accounts, stating poor governance among the reasons for the failure.
The government department came under criticism from the National Audit Office over its potential exposure to losses from Lloyds and Royal Bank of Scotland.
The Treasury's net assets had risen from £2bn in 2007/8 to £44bn in 2008/9, the NAO said.
There are also five other government departments that are to disclose that they have had their accounts for this year qualified by the NAO.
Other bodies which came in for criticism from the National Audit Office included the Home Office, HM Revenue and Customs, the Ministry of Defence and the Department of Work and Pensions.
The Equality and Human Rights Commission was also heavily criticised for making unauthorised payments totalling £323,708 to consultants.
A Treasury spokesman said: "The NAO has acknowledged that the need to act by introducing the Asset Protection Scheme did not allow time to seek parliamentary approval for the accounting consequences of the scheme, which resulted in a technical qualification of the accounts.
"In-principle agreements were not reached with the participating banks until after the final supplementary estimates were laid with Parliament in February.
"They have not expressed concern about the figures for the costs of interventions to support financial stability included in the accounts, which are consistent with the range of £20bn to £50bn set out in the Budget."
