Cardinal Vincent Nichols said that few Christians would be able to make a new life in Britain, even though it is a "fact" they are the most persecuted faith group on Earth.
The British government has promised to take in 20,000 Syrian refugees who've fled Islamic State by 2020, and has already started the resettlement process.
It's selecting from United Nations refugee camps.
However Mr Nichols said that very few Christian refugees use these UN camps, often choosing to go to fellow Christian houses, churches and charities instead, meaning that the vast majority of them will be left behind.
He told the Today programme on Radio 4: "What I'm concerned about is that the programme which the Government has set up about the resettlement, and I can see the point in going directly to the refugee camps, but in fact I think its unintended consequence will be that there will be few, if any, Christians coming to this country.
"That is because for the most part Christian refugees do not go into the UNHCR camps. They go to fellow Christian organisations."
"If we are going to deal purely with UNHCR according to their rules, then there can be no preference given to anybody on behalf of their faith and we will simply bypass the Christian refugees, not intentionally but in fact."
The cardinal also backed the Vatican over its treatment of two journalists still on trial for using leaked information to write books exposing alleged financial impropriety at the Holy See.
He said: "When those [expectations of confidentiality] are manifestly breached then I'm not surprised there is a reaction.
"I think it would be the same in Conservative central office, frankly."
