Joan Smith told the Times newspaper she lost her role as co-chair of London’s Violence Against Women and Girls (VAWG) board after she brought up the issue.
Writer and journalist Ms Smith said she was fired via email after being in the post since 2013.
City Hall denied she was sacked, saying the board had been restructured.
Ms Smith said she had raised concerns about refuges on behalf of charities funded by the mayor’s office and that she had not been consulted about the loss of her role.
She said she wrote to London mayor Sadiq Khan to say that female victims of male violence should not have to share safe spaces with “individuals who have male bodies”. She also said that transgender women should have access to the services they need.
Ms Smith told the Times that she believed she had also “fallen out of favour” at the mayor’s office for calling for improvements within the Met Police to identify sexual predators within the force and “for highlighting endemic misogyny”.
A City Hall spokesperson said: “The Mayor’s Office for Policing and Crime (MOPAC) has undertaken a review of all of its partnership boards, including the VAWG board, to enhance the strategic leadership of the criminal justice system for London and to standardise how all the boards are chaired.
“Our boards bring together a broad range of experts and provide a plurality of viewpoints on the complex issues we are working to tackle. Joan Smith’s expertise and insights on the VAWG board have been valuable and we are grateful for her time and service.”
London’s deputy mayor for policing and crime, Sophie Linden, tweeted in response to Ms Smith’s allegations, saying: “This is simply not true. The structure of all our boards at City Hall is being changed. It has nothing to do with any views Joan has expressed.”
The mayor’s office said all of its boards, including the VAWG board, would now report to the London Criminal Justice Board, chaired by Ms Linden.
An open letter to Mr Khan has been published calling for Ms Smith to be reinstated.