Two registrars at Lambeth Council are under investigation because they swapped shifts in order to accommodate their religious beliefs over homosexual civil partnerships.
The informal arrangement came to light when it was praised as an example of good practice during a diversity training seminar.
But a homosexual colleague complained, and the pair are now being formerly investigated by council bosses.
Other councils have chosen to accommodate the religious beliefs of registrar staff by not forcing them to conduct civil partnership registrations against their will.
But some, such as Islington Council, have chosen to discipline registrars who don’t fall in line.
The complaint against the Lambeth registrars was taken up by Brian Palmer, a homosexual Liberal Democrat councillor, who described their actions as “grossly offensive” and “wholly unacceptable”.
Steve Reed, the Labour leader of the Council, responded by saying that the Council “does not tolerate bigotry for any reason”.
Mr Reed also said that he had asked the council’s chief executive to ensure all staff were aware of their “contractual obligation to provide services equally to all residents.”
Lambeth Council has confirmed that an investigation has been launched, but said that no one had been suspended.
A spokesman for the Council said: “Lambeth Council is fully committed to and supportive of civil partnerships.
“The registrars’ service has never declined to administer a civil partnership enquiry, booking, taking of a notice … ceremony or registration.
“No one has, or ever will in the future, be turned down for a civil partnership for any reason other than that we cannot accommodate the date or time.”
Last December Lillian Ladele, a Christian registrar who was disciplined by Islington Council because of her objections to civil partnerships, lost her case for religious discrimination at the Court of Appeal.
And earlier this year the UK’s Supreme Court refused Miss Ladele permission for an appeal.
The nation’s highest court dismissed the application, claiming that it did not “raise an arguable point of law of general public importance.”
Miss Ladele said she was “disappointed” by the decisions, and felt like her religious rights had been “trampled by another set of rights”.
She is “actively considering” taking her legal fight to Europe.