The children's charity Barnardos has said it is inexcusable for Tusla, the Child and Family Agency, to leave child abuse cases unallocated and ignored.
Its spokesman said the practice increases the risk of harm to other children or of damaging the reputation of innocent people.
The charity has welcomed the decision by Minister for Children Katherine Zappone to ask the Health Information and Quality Authority to undertake an investigation into Tusla's management of child abuse cases.
The minister announced the investigation in the wake of revelations that the agency created and maintained false files alleging abuse involving garda whistleblower Sergeant Maurice McCabe and members of his immediate family.
Yesterday, Ms Zappone said she had apologised to Sgt McCabe and his wife, Lorraine, when she met them last month.
The minister also predicted that the Commission of Investigation, which the Government was planning at that point, would clear Sgt McCabe's name.
In a statement, Barnardos said "scrutiny of processes in how cases are handled is required to ensure lessons are learnt and high standards are kept to the fore".
Barnardos CEO Fergus Finlay said it is crucial the investigation is thorough and concludes quickly to ensure confidence in Tusla is maintained.
"Any failings must be addressed so it is important senior social work professionals play an active role in the investigation.
"Reassurances must be given that any complaints received will be handled robustly, consistently and in a timely manner. It is inexcusable to leave cases unallocated and ignored, thereby increasing the risk of harm to other children or damaging the reputation of innocent people," he said.
He said Tusla had advanced the reform of Ireland's child welfare and protection system since its establishment in 2014 but has struggled from the start with inadequate resources.
"Best practices and processes will always collapse if systems are over-burdened and under constant pressure," he added.
"So the HIQA investigation will not achieve its objective unless the Government accept that our child protection system has the child at its heart and is resourced appropriately."
Earlier, the chief executive of the Irish Society for the Prevention of Cruelty to Children described the involvement of Tusla in the whistleblower scandal as "extremely disappointing".
Grainia Long said there are questions that Tusla has to answer and it was important that things move extremely quickly in order to restore trust.
She said she welcomed the investigation, which needs to start immediately, and should conclude within weeks.
Ms Long added that while she was happy that HIQA was setting the terms of reference, the involvement of child protection professionals in the investigation was really important because it was important to see if there were systemic issues within Tusla.
She said that she has confidence in Tusla but it has been set up with 'one hand tied behind its back' and there are some basics that it is still not getting right.
Confidence, she said, needed to be built, earned and developed.
The Children's Rights Alliance said public confidence in the agency has been knocked by the last week's Prime Time revelations.
Chief Executive Tanya Ward said: "We need to know that when a complaint is made to Tusla about a child that it will be properly investigated and that families will be treated fairly".
She said the McCabe case shows there are still serious issues within Ireland's child protection system, but welcomed the HIQA investigation as a "first step in re-building confidence" in that system.