Boris Johnson has said people attracted to others of the same sex will still be able to receive prayer and pastoral support from churches.
The Prime Minister has written a response to the Evangelical Alliance (EA) after it raised concerns that Christians could face prosecution if the law around the issue was changed.
The EA, along with several other groups, have offered their support to plans to ban conversion therapy but insist freedoms must remain for those who follow traditional Biblical teachings on the issue of sexuality.
In their letter to the PM, the EA's UK Director Peter Lynas warned that a ban would "put at risk the individual freedom of people who are attracted to those of the same sex" and would "threaten the everyday practices of churches, church leaders, and Christians across the UK".
He also called for clarity on the definition of conversion therapy.
Some LGBT campaigners have called for total ban of any practice which seeks to change or surpress someone's sexual or gender identity. That would have included prayer and pastoral support.
Jayne Ozanne is a gay evangelical Christian who founded an organisation in her name that works with religious organisations to eliminate discrimination.
She told Premier last month that a total ban on conversion therapy was a matter of urgency.
"People are being traumatised, people are being hurt right now, often in churches, and other religious settings, and indeed, in medical and mental health practices. We have to bring in legislation to stop this trauma."
Boris Johnson has now confirmed that the reach of any new legislation will not cover prayer or pastoral support.
In his letter to the EA, he said: "I want to reassure you that I take freedom of speech and freedom of religion very seriously.
"As the Government made clear in 2018, when we first made our commitment to end conversion therapy, we will continue to allow adults to receive appropriate pastoral support (including prayer), in churches and other religious settings, in the exploration of their sexual orientation or gender identity.
"Like you, I do not want to see clergy and church members criminalised for normal non-coercive activity."
The Government is yet to outline its plans to ban conversion therapy, though a bill is expected to work its way through parliament later this year.