Siân Berry is to quit as leader of the Greens, citing conflict within the party over transgender rights and claiming it had been a “failure of leadership” on her part that the party was sending “mixed messages”. The Guardian understands there had been a significant clash of opinion with a particular colleague. Berry, who was the party’s candidate for London mayor, had been co-leader with Jonathan Bartley, who announced he was stepping down earlier this month. She said she had been agonising over whether to stand in the forthcoming leadership election but said she felt divisions in the party were too great. A vocal supporter of trans equality, Berry had said one of the first things she would do as mayor would be to set up a commission on the rights of trans Londoners. In her resignation letter on Wednesday, Berry said there had been significant disagreement with colleagues elected to the party’s frontbench team. She said the party’s democratic structure meant decisions could be made that leaders did not agree with and she felt it was irreconcilable with her own position. “There is now an inconsistency between the sincere promise to fight for trans rights and inclusion in my work and the message sent by the party’s choice of frontbench representatives,” she said. “This inconsistency has left me in a very difficult position. I can no longer make the claim that the party speaks unequivocally, with one voice, on this issue. And my conscience simply cannot agree with the argument that there is anything positive in sending these mixed messages, especially when the inclusive attitudes of our membership and wider society are clear.” Berry said she believed failing to change opinion within the party was a failure of her own leadership. “Failing to win the confidence of a majority of my colleagues to reflect these is also a failure of leadership,” she said. “Green leaders do not hold power but we do have a duty to influence, so I must apologise to you all for this failure and hold myself to account.” She said the forthcoming leadership election would mean serious questions must be asked of the party. Berry said: “Will we continue to embrace the principles of listening and solidarity when minority groups are singled out for attack?” One source said Berry had resigned because of a deep moral obligation. “I have a lot of respect for Siân for this, it’s so rare a leader does anything like this,” they said. A Green party spokesperson said it wanted to thank Berry for the “huge role she had in helping to make the Green party the new major force in British politics in the three years she has been co-leader”. The spokesperson said the party was “the most progressive party on issues ranging from trans rights to immigration … It is important that it is our members who decide this policy and it is absolutely right that the party supports trans, non-binary and genderqueer people to live their lives without discrimination or state or medical interference”. He said the party had agreed at its last conference to back a motion that supports self-determination of gender and seeks to remove the heavily medicalised and traumatic process imposed by the Gender Recognition Act on those seeking to update their legally recognised gender. “It is important to recognise that women’s rights and trans rights go hand in hand and the party conference continues to consider policy proposals on this issue,” the spokesperson said. Berry will remain the party’s acting leader until this election is held. The Greens had a record showing in the delayed local elections in May, with a net gain of 91 council seats, taking its national total to a record 444. The party has a role in running 18 councils, and took council seats almost equally from the Conservatives and Labour: 45 of its seats were won from Tory incumbents and 49 from Labour, with a further four from the Liberal Democrats.