Churches and synagogues are being “priced out” of being able to offer civil partnership ceremonies by some local councils who are charging higher fees for the licence needed than for a marriage licence.

Unitarian ministers and liberal rabbis told the Guardian that they wanted to perform civil partnerships, but could not afford the licence fee.

Across the UK, religious institutions are charged £120 for a licence that allows them to perform marriage ceremonies permanently. In three councils, Gloucestershire, Buckinghamshire and Surrey, a licence to perform civil partnerships for three years costs £2,000.

A two-tier system is to blame: a countrywide cost is set for marriage licences for religious institutions, but local councils are allowed to decide how much they will charge the same institutions for civil partnership licences.

As a result, some decide to charge fees similar to those paid by hotels and commercial venues for marriage licences.

The Reverend Andrew Brown of the Memorial Church, Cambridge, said that the costs charged to hotels were impossible for small churches to pay.

“It’s just a prohibitive price, so we didn’t go ahead to offer civil partnerships,” he said. “We haven’t got that kind of money – we’re a small congregation.”

Rabbi Aaron Goldstein of Northwood and Pinner Liberal Synagogue in Hillingdon, London, would have been charged £460 for a three-year civil partnership licence, three times more than the charge for a permanent marriage licence.

He said: “Our synagogue decided not to register itself because of having to pay. We would have reconsidered if there had been immediate demand, but it feels a bit like being penalised for something that should be a right in society.”

The Guardian sampled 42 councils across the country and found that the median cost for a three-year civil partnership licence for religious institution was £1,000.

Several councils said that it would not be fair to charge religious organisations differently to hotels.

The differing charges amount to discrimination and gives another reason to support equal marriage, says Connor Marron of the Coalition for Equal Marriage: “This comes as yet another example of the differences between and marriages, which are not immediately apparent.”