"5,031 emails have been received via the Stand website. 4,856 expressed views against an entitlement card scheme, 44 expressed views in favour," she said.
A further 131 responses contained false information such as made-up addresses she said.
An additional 2,000 responses received by the Home Office showed two-thirds in favour of an ID card and one third opposed.
In answer to a parliamentary question from Adrian Bailey MP, Ms Hughes said that it could take until the middle of next month to fully analyse the responses.
Privacy International, which has been following the ID consultation process closely, is unclear why the government is stalling.
"I don't understand why they need until the end of this parliamentary session to analyse this. There are dodgy tactics going on here," said Simon Davies, head of Privacy International.
He has proposed another public meeting on the issue of ID cards, which are likely to contain biometric information on all citizens and be linked to a national database.
"I proposed it over a week ago but so far the Home Office has not had the decency to reply," he said.
It is widely believed that Home Secretary David Blunkett is in favour of going ahead with some form of national ID card.
The Home Office suspects the overwhelming opposition to the scheme displayed in the public consultation was the result of an organised campaign by Privacy International.
A spokesman said there was a difference between "like-minded people who are positively encouraged to reply" and "individuals who are not connected with the campaign who think through the issues for themselves and write or email their views".
He pointed to a BBC poll for the Morning Show on 22 January which asked "Would you carry an ID card?"
Of the 12,323 people who reponded by phone, interactive TV and online, 89% said yes.
Mr Davies thinks the government's next move may well be a public opinion poll.
He is in favour of such a poll as long as the questions are "detailed, honest and neutral".
"If you ask people if they think an ID card would be a good idea to combat terrorism you will get a very different answer to if you asked whether an ID card is a good thing for Britain," he said.
He believes the government has shown a singular reluctance to discuss the issue of ID cards openly with the public.
"They are avoiding discussions in parliament and if pushed into a corner about the consultation are likely to say that it was held captive by lobby groups," he said.
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