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The council decided in late May to cancel a Speak Up for Women New Zealand event, planned to take place at the Dunedin City Library on June 17.
At the time, the council posted on Twitter that "We strive to ensure our libraries offer an environment where all members of our community can feel welcome and safe".
But this afternoon the council released a statement saying a rescheduled event will go ahead at the Dunedin Centre.
On its Facebook page, Speak Up for Women New Zealand describes itself as a non-partisan organisation that exists to protect and advance the rights and interests of women and girls.
However, the group has been branded anti-transgender by activists.
It has been holding meetings around the country to discuss sex self-identification clauses within the Births, Death, Marriages, and Relationships Registration Bill. A proposal is due to be before Parliament that would allow people to change the sex, as mentioned on their birth certificate, by statutory declaration.
In the council's statement, chief executive Sandy Graham said the initial decision to cancel the event was made on the basis of health and safety concerns, including the welfare of the public, library staff, event organisers, and possible protesters, as well as the potential for damage to the library and its collections.
''When we cancelled the booking, we stated that the DCC strived to ensure that its libraries offer an environment where all members of our community could feel welcome and safe.
''The statement was not intended to convey the message that DCC agreed with any of the characterisations of SUFW which had been posted online.”
In the statement, Speak Up for Women spokeswoman Beth Johnson said the group was pleased the council had clarified its position, ''as our political opponents have been using the cancellation to denigrate our reputation''.
''Today’s announcement from DCC makes it clear that their concerns rest solely on the management of protesters, and not the content or conduct of our meeting.''
The Dunedin meeting will now be held on July 24 in Conference Room 2 of the Dunedin Centre.
Several councils around the country had scrapped the organisation's meetings, leading to a High Court challenge.
Last week the court ruled the group was allowed to hold a meeting in Palmerston North since Speak Up for Women "cannot rationally be described as a hate group".