ID cards will be introduced over the next four years
Mismatched or unclear fingerprints could hamper the government's £5.6bn ID card scheme, independent experts warn.
The Biometric Assurance Group (BAG) says officials may struggle to cope with the number of false matches, which could run into tens of thousands.
Getting clear prints from the over-75s may also prove difficult, it adds.
The government says it is carrying out research into the issues raised - but it rejects BAG's call for iris scans to be used as a back-up to fingerprints.
When the ID scheme was first proposed iris scans were expected to be part of the biometric data stored on the cards.
But the government has now rejected this on cost grounds.
Everyone applying for a passport from 2010/11 will have to submit to a digital fingerprint scan, with the prints to be stored on a database.
They will then have a choice of a passport or ID card which the government says will help them to prove their identity when challenged by the police, border officials or in some commercial transactions such as with banks.
Any false matches - which could result in the wrong person being arrested or prevented from entering the country - will be dealt with manually.
In its annual report for 2007, published this week, the BAG suggests the government has underestimated how much time and effort this will take.
It says dealing with mistakes - called "exceptional handling" - will be a "large part" of the National Identity Scheme's work.
"Exceptional handling has a large impact not only on the technical elements of the scheme but on business processes, schedules and costs," the report says.
It also raises concerns about getting clear fingerprints from the four million over 75s and other people with "challenging biometrics" such as "mute, non-English speaking, blind or visually impaired" people.
In its response, the National Identity Scheme (NIS) said it had funded trials "which investigate the enrolment of people with characteristics that may make biometric enrolment challenging".
It said an enlarged fingerprint bureau was also being planned to ensure mistakes can be corrected quickly.
But the Identity and Passport Service (IPS) rejected a call for iris scan technology - potentially more accurate than fingerprints - to be developed as a fall-back.
"IPS accepts that iris biometric technology has potential but is not inclined to mandate its testing during the current procurement as it is unlikely to be used for scheme launch or immediately thereafter," the DAG report says.
The IPS also rejects claims by one independent expert, Professor John Daugman, of Cambridge university, that false fingerprint matches could reach a rate of one in 1,000.
It said Prof Daugman's research was based on ID card schemes collecting prints from two fingers, where the UK scheme would collect all ten.
The BAG report also raises concern about the "proliferation of different fingerprint readers" to be used by officials which it said could "lead to confusion".
And it urges the government to do more to protect privacy and make sure the public know their data protection rights - particularly as the Identity Cards Act allows some data to be shared with government departments without the consent of the individual.
The IPS said it "accepts the merits of this recommendation".
The report also raises concern about the security of the ID card database, pointing out that officials will be able to access it with just a username and password.
The government said it agreed that "access to sensitive data must be robustly controlled to protect privacy and trust in the scheme".
But it added: "The technical details of the access control solutions which will be used have yet to be resolved".
The BAG report also expresses concern about e-Borders - a new system of electronic exit controls at UK borders from 2009, where passports can be checked against an "alert list" in real time.
It says people stopped as a result of having the same data as individuals on the "alert list" would continually be stopped.
The government conceded this "may occasionally happen but it will not be a common occurrence," the report notes.
Former shadow home secretary David Davis, who is fighting a by-election in Haltemprice and Howden on the issue of civil liberties, said the BAG report demonstrated the "ineffectiveness, intrusiveness and vulnerability of Gordon Brown's ID card system".
"The government will be relying on an utterly flawed mechanism to protect our security, whilst creating widespread chaos and inconvenience for innocent law-abiding members of the public," he added.
"Mr Brown must scrap this expensive white elephant immediately - and contribute the savings to practical measures to protect our security, like a dedicated Border Police Force."
The BAG is a panel of academics and industry experts chaired by the government's chief scientific adviser Sir David King.
It was set up in 2005 to advise the government on the cost, technology and procurement of biometrics.