The disclosure comes a week after the House of Commons Public Accounts Committee, the watchdog of public expenditure, demanded that government departments stop concealing their errors.
The PAC has taken a special interest in failed computer projects after a series of huge losses - including one at Wessex Regional Health Authority which wasted as much as pounds 63m.
The Central Veterinary Laboratory (CVL), part of the Ministry of Agriculture, Fisheries and Food, secretly abandoned a computer system designed to integrate results of tests on animal blood and organs two years ago. The computer was part of an initiative aimed at improving the CVL's efficiency at monitoring the spread of diseases including Bovine Spongiform Encephalopathy (BSE) and salmonella.
Without an integated computer system, CVL officials admit they may sometimes lose specimens or be slow in collating results. The development of the pounds 1.2m system in 1990 was approved by the Treasury. But after a year, the project was abandoned because it was unworkable.
Following an investigation by the trade magazine Computer Weekly, which is published today, the CVL admitted that it had 'lost a lot in terms of time, costs and benefits'. An executive said: 'We were dealing in a completely new area. The suppliers, ourselves and the CCTA (the agency supposed to vet government computer contracts) have made mistakes.'
The decision to scrap the project was not made public and the CVL's annual accounts make no mention of it. The accounts detail the work of the computer department but omit this expense, which was more than the entire annual operating surplus of the CVL itself. Its omission from the budget means that neither the Auditor-General nor the PAC has been made aware of the loss.
Managers refuse to comment on the full extent of the losses, claiming that they are bound to secrecy under the terms of a legal settlement with the computer supplier.