Garage owners have complained they are having to turn away drivers because the system is running slowly or has crashed meaning they may be unable to issue valid MoT certificates.
The Driver and Vehicle Standards Agency (DVSA) said the system has been stuck by an "IT issue" and is asking garages to issue old-style paper MoTs and send the details on.
It comes as the DVSA has switched the issuing of MoTs to a cloud-based system, which uses apps to record the data on phones and tablets.
Paul Watters of the AA said: "We should have learnt from when the electronic MoT was introduced – you would have thought once bitten twice shy. It is a debacle.
"We want drivers to comply with motoring laws. The Driver and Vehicle Licensing Agency (DVLA) and DVSA are moving in the direction of cloud-based applications and I hope this is not a taste of things to come."
This computer glitch has affected an unknown amount of the 16,000 garages which have moved over to the new system.
Frustrated garage owners have complained they cannot get through to the DVSA's help desk or the software company Kainos which was contracted by the Government to carry out the upgrade.
Garage owner Howard Watts, who runs Riddelsdells Garage in Boxford, Suffolk, told the Daily Mail: "We have been having problems since last Thursday and just can't get the system to work.
"It means that we are turning away regular customers who need an MoT - and they shouldn't be on the road without one.
"There have been problems with every new computer system they bring in."
Drivers could risk being stopped by the police for not having a valid MoT even if it has passed so the contingency plans "must be honoured" so that a car can be taxed and "there is no embarrassment", according to Mr Watters.
He said: "We urge drivers to continue applying their cars for the MoT and to take the paper system.
"There will be a backlog and they should make sure they do everything to make sure that drivers and garages are not inconvenienced.
"We need to explore in depth why this project has gone wrong because we know that motoring services are increasingly being delivered in this manner. We support this as long as it works."
DVSA chief executive Alastair Peoples said: "We are aware there has been a delay in some MoT services due to an IT issue. We are working to urgently resolve this and minimise the number of customers affected.
"Contingency plans are in place. MoT certificates can still be processed manually and the online system is still functional.
"Almost 800,000 MoTs have already been recorded using the new online system and DVSA has received positive feedback from industry representatives. The system offers more flexibility for garages as it doesn't require specialist IT equipment, and has significantly lower running costs."
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