Ministers were accused by Labour of encouraging illegal immigrants by ending the practice of fingerprinting those caught trying to enter the UK via the Channel Tunnel.
Immigration Minister Damian Green said the record had proved of little value in practice and that border officials would now have more time to search vehicles for offenders.
But shadow home secretary Yvette Cooper attacked the change and said it sent a signal to stowaways that they should "feel free to keep trying" to enter the UK.
Border security has been under the spotlight since it emerged last year that border controls for non-EU nationals had been relaxed - leading a top official to quit.
Green confirmed the change of policy in a letter to Tory MP Roger Gale after he was alerted to it by a constituent who works for the UK Border Agency.
He said that while fingerprints could identify previously discovered illegal immigrants, it was "generally of limited value in helping to secure their removal" if they got into the UK.
UKBA believed the change "will enable its staff to focus on the high priority of searching vehicles and therefore prevent such individuals from even getting to the UK", he wrote.
A spokesman for the PCS union told The Sunday Times that the end of fingerprinting appeared to be an admission by Green that cuts had left UKBA with insufficient staff.
Calling for an urgent explanation, Cooper said it raised serious concerns about ministers' attitudes to border security.
"By not even bothering to fingerprint anyone, the Government is sending a signal that this is not a serious offence and people should feel free to keep trying. And it makes it harder to identify illegal migrants later on," she said.
"Time and again it seems that checks are being weakened and corners cut."
A UKBA spokesman said: "We work very closely with the French authorities to counter illegal migration - all clandestines are handed straight to the French border police.
"Our controls across the Channel continue to show significant improvements with a 70% reduction in the number of attempts to cross illegally between 2009 and 2011."
Gale said he would raise the issue with ministers when the Commons returns from its Christmas break this week.
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