The trust running the country’s only NHS gender identity service for children is under fire for dismissing a damning internal report that branded it “not fit for purpose”.

Marcus Evans, one of the governors of The Tavistock and Portman NHS Foundation Trust has resigned, after accusing its management of having an “overvalued belief in” the expertise of its Gender Identity Development Service (GIDS) “which is used to dismiss challenge and examination”.

Evans’s decision to part company with the London-based trust, after a 35-year association, will intensify scrutiny of the service which has found itself in the eye of a storm as thousands of young people considering transitioning to another gender seek its help.

Some parents who contacted the Observer have accused the service of “fast-tracking” young people into changing gender, a charge strongly rejected by the service.

Conversely, it has also faced complaints of lengthy waiting times for access to its services and drawn-out assessment periods which the service insists are crucial to understand a person’s needs.

The service has been struggling to contain the fallout from an internal report by Dr David Bell, written in his capacity as then staff governor, which warned that “the GIDS service as it now functions [is] not fit for purpose and children’s ends are being met in a woeful, inadequate manner and some will live on with the damaging consequences”.

In his report, which was submitted to the trust’s board earlier this month and whose findings were first reported in the Observer last year, Bell expressed concern that the service was failing to fully consider psychological and social factors in a young person’s background – such as whether they had been abused, suffered a bereavement or had autism – which might influence their decision to transition. Such views are dismissed by many transgender rights activists who believe they play little, if any, part in a person’s desire to transition.

According to the trust, a review of Bell’s claims by its medical director, Dr Dinesh Sinha, “did not identify any immediate issues in relation to patient safety or failings in the overall approach taken by the service in responding to the needs of young people and families who access its support. As in any review of this nature, it did identify areas for improvement and made several recommendations. The trust’s chief executive is tasked with developing an action plan for how these will be implemented.”

The trust’s 15 governors, who hold its board to account, last week gave their support for it to act on the recommendations. But Evans, a psychoanalyst, subsequently resigned.

“In my 40 years of experience in psychiatry, I have learned that dismissing serious concerns about a service or approach is often driven by a defensive wish to prevent painful examination of an ‘overvalued system’,” he complained in his resignation email.

He added: “I do not believe we understand what is going on in this complex area and the need to adopt an attitude which examines things from different points of view is essential. This is difficult in the current environment as the debate and discussion required is continually being closed down or effectively described as ‘transphobic’ or in some way prejudicial.”

The trust said that it was “confident that Dr Sinha, with oversight from a non-executive board member and a governor, has conducted a thorough and fair review of the issues raised”. It said it intended to publish Sinha’s report and the action plan in due course.

Separately, it has emerged that the trust has agreed to a unique study that will track young people referred to GIDS. It has been awarded £1.3m by the National Institute for Health Research. An independent research team will follow a group of volunteer young people referred to the service, even if they choose to leave it, the first time such a study will be conducted anywhere in the world.

The trust said this would allow researchers to compare outcomes for those who go on to use physical interventions, such as hormone blockers, and those who select an alternative pathway.

“While we know how children and young people are doing in our care, we have struggled in the absence of such research to understand how the care we provide affects them in the longer term and what choices they go on to make as they move into adulthood,” said Dr Polly Carmichael, director of GIDS. “This research, alongside other research that we are conducting, will add to the evidence base around the best ways to support young people with gender dysphoria.”