Identity cards could cost £18bn over 10 years, triple the government's estimate, a draft report has said.
Ministers say ID cards could protect people from identity fraud
This could put the cost to the individual at almost £300 instead of £93, as previously suggested.
A study by a team at the London School of Economics, obtained by The Observer, said the government had underestimated technological and administrative costs.
It said problems such as changing personal details and people refusing ID cards had not been factored in.
The Home Office previously estimated the cost of running the scheme and the biometric passport system to be £5.8bn, the paper said.
But the LSE's report said the true cost could be between £12bn and £18bn, partly because the government did not accurately measure the high cost of technology.
The report said biometric scanners needed to read identity cards would not cost £250 to £750 per unit as the government suggested, but as much as £3,000 to £4,000.
It added that the government had also failed to factor in the financial burden of people changing their personal details.
The report said updating change of address and personal circumstances could result in between 300m and 1.2bn contacts on the register over a decade.
"If human management is necessary to ensure changes are verified, this facet will add between £1bn and £4bn to the 10 year rollout scheme," it said.
It also questioned the government's plan to renew cards every 10 years, saying five years seemed more appropriate.
"All technical and scientific literature indicates that biometric certainty diminishes over time, and it is therefore likely that a biometric - particularly fingerprints and facial features - will have to be re-scanned at least every five years," said the report.
The LSE study also raised the issue of people who are against ID cards, called "refuseniks". It said: "The costs of handling this group will be substantial".
Previously, ministers have stressed they have not yet decided what fees people would have to pay directly to obtain the cards.
Proposals for a national identity card scheme were reintroduced as Labour entered its third term in government.
The plan is for cards to be phased in from 2008, and made compulsory later.
The Home Office has refused to put a figure on the cost of setting up the cards system, saying it is commercially sensitive.