The Rt Rev Dame Sarah Mullally said that for most people, conversion to Christianity was “not like clicking a switch”.
She made the comments in the context of concern surrounding fake conversions.
Last year the Church of England was forced to refuse claims that it operated a “conveyor belt” for fake conversions for asylum seekers.
In February last year it emerged that Abdul Ezedi, the Afghan sex offender who carried out a chemical attack on a woman and two children in Clapham, south London, was granted asylum upon his third attempt after converting to Christianity.
Dame Sarah, 63, who is the current Bishop of London, was announced as the 106th Archbishop of Canterbury last month. She is the first woman to take on the role and will legally become the spiritual head of the Church of England during a ceremony at Canterbury Cathedral in January, followed by a formal enthronement service at a later date.
She has been outspoken on a number of political and social issues during her tenure as Bishop of London.
In her latest intervention, she spoke out regarding conversions as she raised concerns over a call in Parliament for the rejection of refugee claims on grounds of religious persecution where the person converted after arriving in the UK.
She insisted that churches are “not naive” and should not feel anxious about baptising asylum seekers, and ultimately, responsibility lies with the Home Office to process claims, not the Church of England.
Speaking at the report stage of the Border Security, Asylum and Immigration Bill in the House of Lords, she highlighted the persecution and discrimination faced by more than 380m Christians worldwide and the thousands killed for their faith.
“The data on persecution of Christians makes it clear that people are willing and indeed do die for their Christian faith today. We should tread extremely carefully when legislating on such profound matters,” she said.
Conversion for most was “not like clicking a switch”, the bishop told peers and added: “A public declaration of faith is an important moment in that process. But if that declaration may cost you your life or the lives of those that you love, then a person may think very carefully about when and where they make it.
“What better evidence, in many ways, of fear of religious persecution in a country of origin than that a person might wait until they were in the UK to publicly declare their faith.”
She continued: “I imagine that there are some asylum seekers who might well believe that converting to Christianity will help their asylum claim. One can hardly be surprised about that when some politicians keep implying that that is the case.”
However, the Archbishop-designate added: “Clergy are not naive. We train them to do this, to discern the best they can through teaching, through discussion, through reflection, observation and prayer, whether a person, whoever they are, is ready for a public confession of faith through baptism.
“It is not the job of the clergy to assess asylum claims. The Home Office has stated that evidence from clergy or church members in an asylum case does not determine the outcome of the claim.
“I have to say that I am proud that the church into which I am called to serve welcomes, indeed embraces any and all who express a genuine, considered and informed decision to follow Jesus Christ.
“Churches ought not to feel anxious about supporting and baptising asylum seekers if, to their best knowledge, the clergy are confident that there is a sincere desire for conversion, a commitment to Jesus Christ and to discipleship.
“We live in a world in which people regularly die for their Christian faith, and when many hide their Christian faith for fear of persecution.
“Thus, it remains just as important now as it ever has been to offer protection, sanctuary and peace to all those who exercise their right to freedom of belief on our shores.”
Dame Sarah made the comments in response to concerns expressed by former Conservative Home Office minister, Baroness Maclean of Redditch, who referred to reports of “bathtub conversions” in asylum hotels.