Revenue and Customs wrote off almost £11bn in unpaid tax in one year, according to the first joint audit of every government department.
The Treasury was not fully aware of the figure until it appeared in the Whole of Government Accounts (WGA) for 2009 to 2010, according to the Public Accounts Committee.
The PAC said it also had "no knowledge" of whether plans were in place to cut the taxpayer's huge £15.7bn liability for clinical negligence claims.
Its report on the accounts, which were compiled and published for the first time last year. welcomed the potential of the WGA for helping the Government identify the "risks it needs to manage".
But it declared that evidence gathered by officials suggested their understanding of some areas of Government finance was "poor".
The MPs said: "The Treasury should use the WGA specifically to identify key risks to public funds and ensure bodies included in the WGA can demonstrate that they are addressing them effectively."
They added: "We were surprised to find that Treasury did not have a grip on trends in some key areas of risk or plans for managing them."
The committee also complained that the Government had taken 20 months to prepare the accounts, twice as long as other countries such as France and the US.
PAC chair Margaret Hodge said the document also "currently falls short of giving a true and fair view of the UK's financial position".
"The Treasury has departed from accounting standards by leaving out of the accounts of such bodies as Network Rail and the publicly-owned banks," the Labour MP said.
"This has led to the accounts being qualified by the Comptroller & Auditor General. We want the Government to provide the necessary information so that these accounts are comprehensive and credible."
The report highlighted massive swings in liabilities for public sector pensions pensions and nuclear decommissioning and raised concerns about the quality of data.
But the Treasury said the WGA represented "the most ambitious public sector account prepared anywhere in the world" and that it was working hard to remove the qualifications.
"No other country has sought to fully consolidate all public sector bodies, including the local government sector, in one statement of accounts," a spokesman said.
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