The National Gender Service (NGS) has apologised after 109 patient referrals were misplaced.
A full review has taken place of the service, which is based at St Columcille's Hospital in Dublin.
It identified a group of people who should have been seen for their initial visit by now.
However they have not received an appointment date.
The hospital said that due to a "processing error" these people were not allocated appointments, despite being on a waiting list.
"We are aware of 109 people who have been affected by this delay", the hospital said in a statement.
On Tuesday, all those identified in the review were sent a letter informing them of the situation.
The hospital clarified that anyone receiving a letter will be reinstated into the correct position on the waiting list.
![National Gender Service](https://media.radiocms.net/uploads/2019/11/06132025/90227624_90227624-1024x683.jpg)
While each person will also be assigned a case manager from the National Gender Service.
All the people who received a letter can expect a call from their assigned case manager over the next four to six weeks.
"The case manager will answer any questions the affected person might have and help them to get the appointment and support they need", the hospital adds.
The hospital also apologised to those affected, their families and the transgender community.
Transgender Equality Network Ireland (TENI) says it is "shocked" that the patient referrals were misplaced.
The group says: "We understand that these patients have been on incorrect lists for up to three years, waiting on an appointment, without any communication or notification from the NGS."
"We are shocked and disappointed at this disregard for patients.
"This will have a devastating impact on our community. It is a breach of trust."
"Our community told us that they were waiting too long, that their referrals were lost in the system and that they were not being kept informed.
"We knew that these concerns were valid. Now the National Gender Service has finally admitted that their system has failed us."
TENI adds: "Trans people experience a higher incidence of negative mental health outcomes than the general population.
"Poor mental health in our community is often exacerbated by the lack of appropriate gender-affirming health services.
"Trans people deserve accessible and timely healthcare; care that is person-centred and based on international best practice."
TENI held a crisis meeting on Monday with the National Gender Service clinical lead and other members of the NGS team.
Anyone affected by issues raised in this article can contact the LGBT Helpline on 1890-929-539, or the Samaritans at 116-123.