Father John Clark will be using the prayer at Our Lady of Mount Carmel and St Joseph Catholic Church in South London.
Father John said: "We should not forget that Jesus Christ was a refugee. I wonder how Mary and Joseph would be treated if they were to seek sanctuary here today? We must remember in our prayers the refugees who need our protection, but also the civil servants who have to make life-or-death decisions on our behalf."
Development Chaplain Tim Clapton will also be using the prayer at Milton Keynes Mission Partnership. He said: "I am really happy the Churches of Milton Keynes are taking part in the collective prayer for people seeking sanctuary and for those making the life-and-death decisions at the UK Border Agency.
"It's more important now than ever for us to celebrate the diversity of our communities and our proud tradition of offering sanctuary for people fleeing persecution."
Church leaders in the UK expressed their dismay at the advance of radical right-wing parties in the European Parliament earlier this week.
Rachel Lampard, Public Adviser for the Methodist Church, said that the limited success of the BNP had not changed the Churches’ “steadfast” message of God’s universal love.
“God loves all and racism is a sin,” she said. “The campaigning work of the churches and other grassroots organisations has helped to highlight the need for people to vote positively, especially at a time when public confidence in politics has been shaken.”
The Rev Graham Sparkes, Head of Faith and Unity for the Baptist Union of Great Britain, said it was “deeply disappointing” that a racist party would be representing Britain in Europe for the next five years.
He said it was vital that the remaining UK representatives “dedicate themselves to promote the common good”.
The United Reformed Church’s Secretary for Church and Society Frank Kantor said: “We must never become comfortable with the BNP using their position to promote their racist policies. We will continue to counter their messages of hatred and fear.”
The BNP had come under fire from Churches in the run up to the election after launching a poster campaign featuring Jesus and quoting Scripture.
The Archbishops of Canterbury and York were among the Church leaders who publicly distanced themselves from the BNP’s Christian language.
