The Home Office is being accused of showing "casual disregard for taxpayers' money" after a spending watchdog criticised its accounts.
Sir John singled out the Home Office for particular criticism
The National Audit Office said it had not had the evidence to form an opinion on the accounts for 2004/5, and there were fundamental problems with them.
Tory MP Richard Bacon, a member of the Commons public accounts committee, called the failings "unacceptable".
The Home Office says it has worked hard to put the problems right.
The department is criticised in Auditor General Sir John Bourn's report on government accounts for 2004/5.
Sir John said departments were generally making good progress in improving the quality of their accounts - and keeping to deadlines.
But many of them still needed to make "significant improvements".
He issued qualified accounts on two departments, compared to four the previous year.
They were the Home Office and the Department of Work and Pensions.
There were such "such fundamental problems" with the Home Office's accounts that he had to issue a "disclaimer of opinion" because of the lack of audit evidence needed to assess whether they were truthful and fair.
The Home Office had not kept complete financial books and records during the year and so was unable to deliver its accounts for audit on time, he said.
Mr Bacon said the Home Office had shown "casual disregard for the use of taxpayers' money".
Sir John Gieve, former top civil servant at the Home Office and now deputy governor of the Bank of England, should have to explain the "mess" to Parliament, he said.
He asked how the public could be confident their money was being used well on such projects as ID cards and the merger of local police forces.
"It is simply unacceptable that we have been left in the dark over how the Home Office is using our money," he said.
A Home Office spokeswoman said the department's new permanent secretary and finance director were fully committed to resolving the problems.
"A great deal of work has been done over recent months to put right the problems highlighted by the NAO which arose from the introduction of a new accounting system in 2004-05," she said.
"We have strengthened our system controls and financial accounting; we have more than doubled the number of qualified and experienced accountants and we are relocating the financial accounting function to our London headquarters."
The Home Office is also asking a firm of accountants to undertake an "urgent review" to see whether extra measures are needed.