In guidance to MPs, the Equalities and Human Rights Commission (EHRC) said marriage registrars were public officials and so should expect to be “required” to carry out the ceremonies.
The document makes clear that employees, including teachers and chaplains working in the public sector, should be free to express their views on marriage without being disciplined.
But it says that religious protection is “a qualified right” which “the state can interfere with” in some circumstances.
The question of whether council registrars can object to carrying out parts of their jobs if they clash with their religious beliefs was thrown into the spotlight by the case of Lillian Ladele, who was one of four Christians who went to the European Court of Human Rights last year over disputes involving their employers.
Ms Ladele, a former registrar from Islington, north London, was refused the right to opt out of performing civil partnership ceremonies which went against her traditional beliefs about the teaching of the Bible.
She accused Islington Council of discriminating against her on grounds of religion and initially won her case at an employment tribunal.
But that decision was overturned on appeal, in favour of the council which argued it had to prevent discrimination against gay people.
That position was then upheld last month by the European Court in a controversial split decision.