Home Secretary David Blunkett has defended the policy of detaining terror suspects without trial after it was criticised by Dr Rowan Williams.
Dr Williams opposed war in Iraq
Mr Blunkett told BBC Radio 4's The World This Weekend that he had a duty to protect people from terrorists.
Earlier, it was revealed that the Archbishop of Canterbury is to use his Christmas speech to say the policy could make Muslims feel targeted.
Fourteen men are being held in a London prison under the emergency legislation.
The power to detain without trial foreign terror suspects who could not be deported was introduced two years ago after September 11.
Mr Blunkett told the programme the men being held in Belmarsh prison in London were not being detained because they are Islamic.
He said: "I am not interested in the religious commitment or the religious background of the individuals concerned, any more than we were in terms of those who committed atrocities in the name of Irish nationalism were Catholics.
"I am interested in whether they are terrorists."
Dr Williams also criticised the US for similar action in imprisoning 660 suspects, including nine Britons, in Cuba.
But Mr Blunkett said there was no comparison between the two because those held in the UK had legal representation and a right of appeal on a point of law.
He said: "We would be very happy if the nine British citizens held in Cuba went
through the kind of process we have established with the agreement of
Mr Blunkett said he was conducting a review of the detention system for next year and would be happy to hear from critics such as the Archbishop.
Dr Williams's reference to Islam in his first Christmas sermon as Archbishop of Canterbury is a surprising departure.
Speaking to the Sunday Times newspaper,Dr Williams said their plight was jeopardising the efforts of moderate Muslims to foster democracy and religious tolerance in places like Iraq.
Nine British Muslims are imprisoned in Guantanamo Bay, Cuba
"If we want to persuade moderate Muslims to sign up to toleration and pluralism of the right kind, anything that gives the impression that we are targeting Muslims is problematic.
"We have a lot of ground to make up."
The Archbishop's comments have found support among British Muslims.
Muslim News editor Ahmed Versi told BBC News: "The Muslim community feel that they are under siege. They believe that they are being targeted by the government.
"They believe that these are just fishing expeditions."
Dr Williams has made improving the dialogue between Christianity and Islam a priority during his first year as leader of the worldwide Anglican Church.
He was among the most vehement critics of the war in Iraq.
Dr Williams told the Sunday Times a three-day seminar of 30 Christians and Islamic scholars he had hosted in Qatar during the conflict had showed "you can have public disagreement and mutual respect".
He is also set to use Wednesday's sermon to attack last week's decision by French President Jacques Chirac to back a ban on religious symbols in schools.
He says it would be a "very provocative and very destructive" move.
"There is no such thing as a neutral public space in which everybody has to put aside that which makes them distinctive."