Equalities minister Harriet Harman could remove an Equality Bill amendment allowing civil partnerships in church over fears it could raise problems in the marriage system.

The amendment, tabled by out gay peer Lord Alli, was approved by the Lords this week.

But the Daily Telegraph reports that there are fears it could raise problems for faith groups, priests, registrars and heterosexual civil marriages if it becomes law.

A Whitehall source told the newspaper: “It hasn’t been decided yet – it’s possible that the government will try to remove the amendment in the Commons.”

During debate in the Lords, some peers argued that civil partnerships, by their name, were not supposed to be religious and that the point of civil heterosexual marriages were that they were not allowed in churches.

The 2005 civil partnerships legislation banned any religious aspect in the ceremonies. The amendment was tabled after faith groups such as the Quakers, Unitarians and Liberal Judaism expressed their wishes to hold the ceremonies.

The government has only weeks to pass the Equality Bill before a general election is called.

The Daily Telegraph speculated that Ms Harman will allow the amendment to be voted through the House of Commons and will then begin a consultation on changes to civil partnership and civil marriage regulations.

If passed into law, the amendment would give faiths the option of hosting civil partnerships, rather than forcing them to do so.

Yesterday, the Bishop of Winchester Michael Scott-Joynt claimed that gay couples could use human rights legislation to sue vicars and other faith leaders who chose not to officiate for them.