Some Anglican priests say they would rather be sued than allow people who have changed their sex to marry in their churches.
Clergy could opt out of performing the ceremonies themselves
The Gender Recognition Bill, soon to become law, will oblige marriage registrars to give equal rights to transsexual people.
A conscience clause will allow clergy to refuse to carry out such weddings.
Members of the Anglican group Reform do not want such ceremonies to be carried out in church buildings at all.
They fear it could establish a precedent that paves the way for same-sex blessings, or even marriages.
But the move has been welcomed by more liberal Anglicans, who say transsexual people only want the same rights that others take for granted.
Claire McNab, vice-president of the campaign group Press For Change, said: "It is mischievous nonsense to claim that the Gender Recognition Bill forces The Church to marry transsexual people.
Emma Martin says the Bill will help her live a 'real' life
"On the contrary, the bill provides an explicit opt-out for Anglican clergy, who are the only clergy under any legal obligation to marry anyone.
"These anonymous clerics are trying to use the law to prevent their less prejudiced colleagues from marrying transsexual people.
"They want freedom for their consciences, but not for other priests."
'Open to risk'
Under the legislation people who have sex-change surgery - or who convince a qualified person that their body does not represent their true gender - gain the right to have their new sex recognised.
Emma Martin, who was born as a man but changed her sex three years ago, said the issue was simply one of equality.
"It's about allowing us to live our real lives, rather than forcing us to live half a life," she told BBC News.
But traditionalists believe the law could leave them at risk of marrying people of the same sex, saying that surgery does not automatically create a change of gender.
Reverend Rod Thomas, of St Matthew's Church in Plymouth, told BBC News: "We could not in conscience approve of that and we would be obliged to allow our building to be used by the law. If we refuse we could be sued."
A spokeswoman for the Department for Constitutional Affairs confirmed that a couple, one of who was a transsexual, would be allowed under the new law to marry in a church.
'Free from obligation'
Whether or not a member of the clergy could prevent this happening was, she said "a matter for the Church".
She stressed that the bill would free members of the clergy from their obligation to carry out this sort of marriage on theological grounds.
"We have worked with the Church on this and the established Church in England and Wales are satisfied with the conscience clause.
"If an individual did not want to marry the couple, it could be done by another member of the clergy."
A transsexual person was not obliged to reveal their personal history, she added.
"Under the new law, marriages contracted by transsexual people once their change of gender has been legally recognised will be valid marriages between a male and a female - not same-sex."
The government has said it has no plans to introduce same-sex marriages.