A number of doctors have claimed a service under which adolescents with gender dysphoria can be given puberty-suppressing hormone blockers is "unsafe" and must be immediately stopped, but their concerns were suppressed.
The service is provided in Ireland by flying in two clinicians from an NHS trust in London to run clinics at Crumlin Children's Hospital.
But the Irish Independent has learned at least three doctors working in the gender area expressed grave concerns over the service provided by the Tavistock and Portman NHS Foundation Trust at Crumlin.
The concerns over standards of clinical care and governance were raised at a meeting of doctors and hospital officials in Crumlin last March.
These included that children had been started on hormone treatment when they did not appear to be suitable.
However, the issues raised and calls by the doctors for the service to be "terminated with immediate effect" were omitted from draft minutes of the meeting.
Something of a standoff has ensued since then, with the HSE claiming their concerns were "not representative of the many clinicians who refer to the Tavistock". Transgender Equality Network Ireland (TENI) has also said it does not have any concerns about the service provided in Crumlin.
Some 291 Irish children have used the service since 2015.
The doctors who raised concerns are consultant endocrinologist Professor Donal O'Shea and consultant psychiatrists Dr Paul Moran and Dr Ian Schneider. All three are attached to the adult national gender service at St Columcille's Hospital in Loughlinstown, Dublin, which deals with adult referrals, including children previously treated at Crumlin.
News of their concerns comes days after it emerged a lawsuit was being taken by a former nurse, a parent, and a former patient against the trust in the London High Court. The action is challenging the clinic's practice of prescribing hormone blockers and cross-sex hormones to children under the age of 18.
The trust has also been hit by a series of resignations by psychologists amid disquiet about the alleged "over-diagnosis" of gender dysphoria.
Details of what transpired at the meeting were confirmed by Prof O'Shea and Dr Moran after they were contacted by the Irish Independent.
In a statement, Dr Moran said they were concerned some patients they were seeing, who had been started on hormone treatment in Crumlin, did not appear to be suitable or ready for such treatment, and appeared to have mental health problems that had not been identified or addressed.
He said that for many children on hormones, there was no documented report or assessment by Tavistock, and where these were available, they were not sufficiently detailed and not a sound basis for a treatment recommendation. "There was usually no clear record of how or when the decision to commence treatment was made," he said.
Dr Moran raised questions over the clinical governance of the service and said the funding for it was also irregular.
He said it was funded under the EU Treatment Abroad Scheme, which is used to fund treatments outside the country, but most of the children were being treated in Ireland.
He also said that when he protested about the omissions in the draft minutes, these were not corrected. A query regarding the minutes was not addressed by the hospital.
In a statement, the HSE said it was satisfied with the arrangements in place and that the service was in line with the terms of the Treatment Abroad Scheme.
It said the trust "records thorough notes on each patient", which are shared when they are referred to the consultant endocrinologist delivering transgender care in Crumlin. It said the notes also form part of onward referrals to the adult gender service.
The HSE said it was planning to develop an entirely Irish-based service "within the next year" and was working with leading clinicians and representatives of the transgender community to develop an agreed model of care.