The Catholic church is on a collision course with the government after declaring it will oppose in the "strongest terms" changes to the Equality Act that will allow gay couples to register civil partnerships in places of worship.

A statement from the archbishop of Southwark, the Most Rev Peter Smith, said it was neither "necessary nor desirable" to allow gays and lesbians to have civil partnership ceremonies in religious premises and accused the government of "considering a fundamental change to the status of marriage".

Churches and Christian groups have criticised the Home Office decision, announced last week, to lift the bar on civil partnership ceremonies being held in places of worship. The equalities minister, Lynne Featherstone, has come under fire for disclosing the government's intention to consult over how marriage laws in England and Wales can be reformed further.

The home secretary, Theresa May, said the rule changes would not be mandatory: "No religious group will be forced to host a civil partnership registration, but for those who wish to do so this is an important step forward."

But Smith said the change was something "never envisaged by the Equality Act or any other legislation passed by parliament".

The archbishop added: "Marriage does not belong to the state any more than it belongs to the church. It is a fundamental human institution rooted in human nature itself. It is a lifelong commitment of a man and a woman to each other, publicly entered into, for their mutual wellbeing and for the procreation and upbringing of children."

There was also implicit criticism of those religions and movements supporting the change – Quakers, Unitarians and Liberal Jews have welcomed the government's modernising agenda.

Smith said: "No authority – civil or religious – has the power to modify the fundamental nature of marriage.

"The Equality Act was amended to permit civil partnerships on religious premises, which unhelpfully blurs the distinction previously upheld by parliament and the courts between marriage and civil partnerships.

"A consenting minister is perfectly free to hold a religious ceremony either before or after a civil partnership. That is a matter of religious freedom, but it requires no legislation by the state. We do not believe it is either necessary or desirable to allow the registration of civil partnerships on religious premises. These will not take place in Catholic churches."

The Catholic bishops of England and Wales have had mixed success when they have lobbied government in the past.

In 2006 they succeeded in persuading the then education secretary, Alan Johnson, to scrap plans for quotas in faith schools, but failed to persuade the Labour government in 2007 that Catholic adoption agencies should be exempt from sexual orientation regulations, which would have led them to consider gay couples as prospective parents.

The Lesbian and Gay Christian Movement, a UK-based international and non-denominational charity campaigning for an inclusive church, welcomed Featherstone's announcement.

Its chief executive, the Rev Sharon Ferguson, said: "We are of course delighted by this development which has been a long time coming. We reject concerns by some that this is an infringement upon religious liberty. No religious group, Christian or otherwise, will be forced to conduct civil partnerships. But the current situation is an infringement upon the religious liberty of those faith groups who are happy and indeed keen to conduct such civil partnership ceremonies."