Children At Risk in Ireland (CARI) national clinical director Eileen Prendiville said that the first 48 hours following a child's disclosure of sexual abuse had the greatest impact on their potential to heal.
Ms Prendiville said children could be waiting more than a year to be assessed because of a lack of resources to deal with cases. "No child should have to wait that long," she said.
Ms Prendiville said the situation was not helped by parents being warned, usually by social workers, not to talk to the child in case they interfered with a possible criminal case against the alleged offender.
"It means that the child is not having his or her emotional needs met and, perhaps, his or her safety needs as well."
While CARI is not able to meet a child who has said he or she has been abused until after a health board assessment, it does see the child's parents and will work with them to ensure that the needs of the children are being met.
"Parents really don't know how to cope when the child starts to have nightmares or temper tantrums and they are really worried that their child might be taken away from them."
Parents who contact CARI are offered an appointment at a venue that is closest to them as soon as possible, usually within a week of phoning.
"We will work with the parents right through the process and help them negotiate the system," Ms Prendiville said.
Muireann Ó Briain of the Dublin Rape Crisis Centre said health boards were finding it particularly difficult to find qualified clinical people to validate children's reports of sexual abuse.
Because of what happened to Dr Moira Woods, who pioneered the treatment of child sexual abuse in Ireland, doctors were afraid of reporting child abuse, a situation that was contributing to the logjam, she said.
Just over a year ago, Dr Woods was found guilty of professional misconduct by the Medical Council's Fitness to Practise Committee relating to her diagnosis of sexual abuse of children in three families in the 1980s. Allegations relating to six other children were found not to have been proved.
The Eastern Regional Health Authority (EHRA) says that "priority" cases are usually seen within three to four months. Other cases, not meeting the priority criteria, have to wait up to seven months.
Currently, Our Lady's Hospital for Sick Children in Dublin has 68 children waiting to be assessed at the Hospital's child sexual abuse unit.
An EHRA spokesperson said the Department of Health and Children had asked them for a complete review of the situation.
A spokesperson for the Southern Health Board could not give an average waiting time it took for abused children to be assessed at the child sexual abuse unit based in St Finbarr's Hospital in Cork.
Less than 20 children are waiting to be assessed at the unit. The spokesperson said the cases were prioritised and some children could be seen straight away.
The CARI helpline number is 1890 924567.