The Health Service Executive took two months to arrange a specialist medical examination for an 11-year-old girl who claimed she was violently raped on several occasions, according to a report by the Ombudsman for Children.
It says the actions of the HSE contributed to an adverse effect on the child, who did not receive therapeutic support.
The HSE also failed to appoint a social worker.
Between December 2006 and July 2007, the girl made disclosures of multiple instances of severe child abuse.
She alleged repeated instances of violent rape by a man, which involved death threats with a knife.
The child underwent detailed interviews with gardaí over several months.
The child's mother reported her daughter's threatened suicide and depression around the time of the disclosures.
In May 2009, the mother complained to the Ombudsman for Children about the HSE's response in the case.
The report says that within the first 72 hours of an instance of sexual abuse or rape, there is a higher probability that a specialist medical examination will yield evidence that may be significant.
In February, the mother asked the HSE to conduct a medical examination.
Initially, the HSE arranged for a male specialist to perform it, but the child felt it would be too stressful with a man.
It took two months for the HSE to find a female specialist to do the examination.
In June 2010, the Director of Public Prosecutions decided not to mount a criminal prosecution in the case.
The report says the allegations had been made two days before Christmas in 2006 and two weeks had passed.
The HSE decided not to allocate a social worker, citing capacity and procedural reasons.
It said that allocating a social worker would be uncommon, unless there was an ongoing risk to the child.
The mother sought therapeutic support from a private specialist.
The report also found the HSE's actions and contacts in the case were not recorded contemporaneously, or in a uniform or consistent fashion.
Information is also missing from the case notes.
The Ombudsman said the HSE failed to consider the child's best interests as a primary factor.
The child was present for some of the arguments that occurred between the HSE and her mother on the telephone in 2006 over support.
Seven years on, the child does not trust the HSE and feels betrayed by its actions.
HSE's actions may be result of negligence - Ombudsman
Ombudsman for Children Emily Logan has found the actions of the HSE may have been as a result of negligence.
Ms Logan recommended that the HSE continue to engage with the child and mother in order to assess the child's current needs.
She said it should also prioritise direct contact with children and have face-to-face contact with families.
Speaking on RTÉ's News at One, Ms Logan said the HSE's perception of the girl's mother as "difficult and challenging" became an impediment to ensuring the child's interests were paramount.
She said that during her investigation she had formed the view that the mother was a person of great capacity who would work hard to get her daughter the resources she required.
The report says the HSE should allocate a social worker to complex cases and improve its record-keeping.
It should also streamline the system for organising medical examinations and ensure a gender balance of physicians.
HSE accepts Ombudman's report
The HSE has said it has accepted and is currently implementing the recommendations made by the Ombudsman in her report.
It said that since the allegation was first reported in 2006, the provision of services and national practices in relation to child sexual abuse have evolved and improved significantly.
These improvements include the assignment of extra social workers and dedicated sexual assault treatment units, which are available on a 24-hour basis with access to female consultants.
The HSE said that it works under agreed protocols with gardaí to ensure that allegations of child abuse are investigated in accordance with statute and in compliance with Children First.