Government plans to introduce a ban on so-called conversion therapy must not infringe upon religious freedom, the equalities body has warned.
In a major intervention, the Equality and Human Rights Commission (EHRC) said, "Encouraging people to comply with religious doctrine that requires refraining from certain types of sexual activity should not fall within the definition of conversion therapy either."
The equalities watchdog also warned of a "chilling effect" on therapists, and said that parents and teachers are at risk of being criminalised if they question a child's desire to change gender.
The EHRC raises concerns that the consultation does not address "the possible need to consider a differentiated approach in relation to sexual orientation and being transgender so as to ensure, in particular, that clinicians and therapists are not prohibited from providing appropriate care and support for individuals with gender dysphoria."
This should include the freedom to help people accept their gender, the watchdog said.
"The Government should make clear that psychological, medical and healthcare staff can continue to provide support to people experiencing gender dysphoria; this should include support to reduce distress and reconcile a person to their biological sex where clinically indicated, including for children and young people aged under 18 if this is in their best interests," it said.
The EHRC said ministers should postpone the ban until legislation has been amended to ensure basic freedoms are safeguarded.
The intervention has been welcomed by The Christian Institute's Simon Calvert who said the government needed "to give clear, legally-watertight answers to the EHRC's questions about how they plan to protect our basic right to pray and talk with friends about our beliefs".
"Christians must not be put at risk of prosecution just for inviting LGBT people to embrace the Christian faith," he said.
He agreed with the call to pause legislation.
"These warnings from the Equality and Human Rights Commission confirm our fears that getting this legislation wrong could be deeply damaging for basic religious freedoms. And they also confirm that the research basis for the proposals is poor," he said.
"The government is rushing headlong into a human rights minefield. It needs to pause and take the time to get this right."
The Christian Institute has already threatened legal action against the government if the ordinary activities of churches are criminalised.
Mr Calvert added, "We took advice from leading human rights QC, Jason Coppel, who confirms that Christian beliefs on sexuality are protected by human rights law.
"Our lawyers have made clear to the Equalities Minister that we are prepared to seek judicial review if the Government gets this wrong and brings in a ban which includes the ordinary, everyday activities of churches."