A software glitch led to around 62,000 duplicate tax discs being sent out from the Driving Vehicle and Licensing Authority (DVLA).
Drivers who applied for a tax disc on 11 April this year via a system run by IBM were sent two discs a few days apart.
The DVLA said it had cancelled the erroneous discs and had sent out a letter of apology to those affected.
The problem is not thought to have lasted longer than a day.
A spokesperson said, "As a result of an error, a number of customers who recently purchased tax discs online or by phone, were issued with duplicate discs.
"Once the problem was identified, swift action was taken to rectify it. All customers affected are being sent a letter of apology and the erroneous discs have been cancelled."
The DVLA's online car tax system has previously been lauded as one of the government's more successful IT projects. It does more business on the web than Tesco, with a third of motorists buying their car tax online. The organisation is hoping the system will save it £50m in the eight years between 2007 and 2015.