A transgender employee of the Guardian — which once called itself the “world’s leading liberal voice” — has resigned, accusing the newspaper in an email to staff of being “an incredibly transphobic organisation”.

In a cutting resignation letter sent last month, the employee said the paper “fundamentally not only stands against my own values but also against what I am”. A second trans staff member resigned weeks later, also citing the “harm” they say the newspaper is doing to trans people.

Following the leak of the email to BuzzFeed News, the trans employee, who spoke on the condition of anonymity, said she felt complicit in the newspaper’s "transphobic" reporting by continuing to work there, and revealed the damaging effect the Guardian’s coverage of transgender people has had on her well-being. This included fear of using the women’s toilet at work.

Such editorial lines, she said, are a “blind spot” for the largely progressive publication, which last month published a long read criticising other news outlets for their stigmatizing coverage of refugees, another marginalised group.

The former employee also said colleagues had made transphobic remarks to her.

Her resignation marks a flashpoint in what multiple sources at the Guardian have described to BuzzFeed News as a deepening internal war over the rights of transgender people — and how the organisation reports on them. Staff members across several departments accused the paper of “institutional transphobia”, peddling transphobic tropes, and allowing a bitter schism to develop between pro- and anti-trans journalists.

The resignation email, sent by the employee whom we will call Victoria, was the culmination of months of wrangling over the subject at the newspaper which, she said, helped push her towards the exit. She warned that the paper would lose more talent and alienate younger readers if it did not change course.