After they have converted, they tell the Home Office their new faith would open them up to persecution such as torture, or even execution if they are deported back to their home country.
Church leaders said being baptised can “significantly enhance” asylum seekers’ odds of being granted refuge in the UK.
The Reverend Pete Wilcox, Dean of Liverpool, said the cathedral has baptised roughly 200 asylum seekers in the last four years.
He said: “Mixed motives are not unheard of.”
The vicar said it was similar to parents getting their children baptised to ensure they get a place at a church school.
He added: “God alone knows the person’s heart and we try to be consistent about that and not to set the bar at one height for middle-class aspiring parents seeking the best for the education of their children and the bar at another height for converts from Islam looking for asylum.
“Refuse Jemima baptism and she goes to school somewhere else.
“Refuse Mohammed baptism and he gets deported.”
On the other hand, he said there is no comparative rush for British citizens to convert to Christianity from Islam.
He added: “I can’t think of a single example of somebody who already had British citizenship converting here with us from Islam to Christianity.”
The vicar said having a baptism certificate “significantly enhances” their asylum claim.
Reverend Wilcox, said: “Once you are a baptised Christian it is really not conceivable that you would be deported to a Muslim country.”
Anybody converting to Christianity at Liverpool Cathedral has to take part in a five-week baptism course and have to attend church services before it starts.
Another seven vicars at churches across the UK confirmed they have baptised hundreds of Muslims, mostly from Iran.
Over the past four years, Stockton Parish Church in Stockton-on-Tees has baptised 100 Iranians, with vicar Mark Miller, saying he did not think any British adults or children had been baptised there in the past year.
At Elim Pentecostal Church in Liverpool about 300 Muslims, also mainly from Iran, have been baptised since 2010, with 100 known to have used it to help them stay in the UK.
Another 50 Muslim asylum seekers converted to Christianity at All Saints Church, also in Liverpool.
The Border Agency contacted vicar Mike Coates to check on claimants and said he has told asylum seekers: “We will not lie for you.”
There are no allegations against vicars acting improperly or failing to make honest judgements on whether people are truly wanting to convert or are doing it for immigration purposes.
A Home Office spokesman said each asylum claim is considered individually.
He said: “A document such as a baptism certificate would not automatically lead to a conversion claim being accepted as genuine but is given appropriate weight when considering all the evidence.”
A spokesman for the Church of England said: “Baptism is open to all of whatever background, class, nation, sexuality or age.”