Information equipment introduced at 82 Training and Enterprise Councils in England and Wales was also found to be complicated and difficult to operate, the government spending watchdog found.
The remarks are the latest in a series of attacks on ministers over the purchase of new technology involving the expenditure of at least pounds 200m of taxpayers' money.
In his report Sir John Bourn, Comptroller and Auditor General, said the system had been only a 'partial success' and was the 'source of friction' between the TECs and the Government.
The so-called 'Field System' was developed by the Department of Employment specifically for TECs, which are responsible for nearly pounds 2bn of state spending on vocational training, largely for the unemployed.
Last month the Department of Health was accused by doctors of wasting an estimated pounds 86m on poorly regulated and incompatible information systems for GPs.
At the end of last year, Robert Sheldon, chairman of the Commons Public Accounts Committee, accused the Government of a 'slap happy' approach to the introduction of computers into Whitehall departments and state-funded services.
The National Audit Office says in yesterday's report that the Department of Employment experienced 'significant problems' in developing and implementing the system.
Many of the councils were not using it to its fullest extent. 'Weaknesses in management and control compounded the problems that affected the project,' the report says.
Computer Systems for Training and Enterprise Councils: The Department of Employment's Management of the Field System; HMSO; pounds 7.40.