Between 7 and 10 per cent of the MoD's systems - up to 150 of them - are being examined on a random sample basis in an audit due to be completed in October.
Testing by external computer experts showed that 15 per cent of those so far examined were suffering from severe problems, while a further 20 per cent had minor deficiencies.
Inquiries by auditors also established that fewer than half of the MoD's suppliers had confirmed that their systems had been cleared of glitches.
The MoD insisted last night that the failures, discovered by programmers from Logica and Smith Systems, were being tackled and did not involve nuclear or other key weapons systems.
But anti-nuclear campaigners said the failure of equipment, which had already been declared safe, did not bode well for the millennium.
The findings of the audit have been presented to the Cabinet by the Central Computer and Telecommunications Agency as part of a pounds 200m programme to ensure that Britain is "Y2K"-compliant. Many computers and other pieces of equipment may fail if their embedded chips do not recognise the zeros in the date 2000.
In response to inquiries by the agency, the MoD replied: "Of these [systems examined], some 65 per cent were satisfactory, 20 per cent were found to have minor deficiencies (minor deficiencies are where the auditors concluded the work completed was adequate to demonstrate compliance, but aspects of the project needed further attention).
"Fifteen per cent were found to have major deficiencies (in these cases the audits concluded that further work was needed before the system could be declared to be compliant)."
Asked whether it had enough staff with the expertise to cope with the problem, the MoD replied: "Shortfalls are being encountered. Where necessary, consultancy support is being used to supplement in-house resources."
It added: "Shortage of skilled in-house staff has been identified as a potential risk to the programme across the MoD."
Perhaps more disturbingly, many suppliers and contractors, over which the MoD has little hands-on control, have failed to prove they are Y2K- compliant.
The MoD wrote to 600 suppliers, asking them to confirm that they could supply goods and services over the millennium period. Only two-thirds bothered to reply. Of these replies, only 49 per cent were described as "satisfactory".
William Peden, parliamentary researcher for the Campaign for Nuclear Disarmament, said: "They [the MoD] have been assuring us for some time now that certain computer systems will be safe over the millennium and now we find out that they're not.
"They also assure us that our nuclear deterrent is safe. But now how can we be sure?"
The MoD, however, said Britain's Trident nuclear deterrent was 100 per cent safe and the deficiencies highlighted did not involve weapons systems. A spokesman said the problems mainly involved stores systems.
"We are confident that our defence capabilities will be maintained throughout the Y2K period," he said.Reuse content