Garda superintendents have called on the Chairperson of the Garda Ombudsman to clarify comments made at the Oireachtas Justice Committee.
Ms Justice Mary Ellen Ring said the Ombudsman finds it troubling that gardaí continue to conduct criminal investigations of its own members without the knowledge or participation of GSOC.
Ms Justice Ring told the committee that GSOC had become aware - along with the public - of allegations of garda wrongdoing through the media.
"We are aware that the gardaí continue to conduct criminal investigations of its own members without the knowledge or participation of GSOC and we find that troubling," she said.
Ms Justice Ring said the practice runs the risk of allegations of cover up or bias or corruption when it becomes known that such investigations have been carried out internally.
"It runs the risk that fair and independent investigations are not seen as such by the public because they were not notified outside the organisation," she added.
However, the President of the Association of Garda Superintendents rejected this and said this did not make sense and called for clarification.
Noel Cunningham was speaking at the association's annual conference.
Supt Cunningham said such a claim did not make sense because a criminal investigation, by its nature, involved outside parties such as witnesses and legal representation and there could be no question of a cover up.
He also highlighted the fact that while on the one hand GSOC were seeking to be informed of every investigation, they still sent the majority of their cases back to Superintendents to be investigated.
Some officers, he said, had up to 20 investigations to carry out and had to refuse others and the problem is that GSOC has never been properly resourced to deal with all such investigations.
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Ms Ring also told the committee that GSOC received 24 new protected disclosures from gardaí in 2018, in comparison to 11 protected disclosures made to the gardaí during that year.
She said the handling of protected disclosures within the garda organisation was an area of great concern.
"GSOC sought, and obtained, an increase in our numbers for these very important investigations.We have set up a separate unit with separate facilities and the last of the sanctioned investigators joined the unit in the past week".
"GSOC would be of the view that the continued growth in protected disclosures made to GSOC indicates one of two things - a growing confidence in GSOC to treat these disclosures respectfully or a lack of confidence in the Garda Síochána to investigate such disclosures".
Independents4Change TD Clare Daly said Ms Justice Ring painted a depressing picture about the pace of progress in relation to protected disclosures.
In relation to the handling of protected disclosures, Ms Ring said it was possible that GSOC could be investigating a complaint that the gardaí could also be investigating, but they may not be aware of this.
"It seems to me if we are going to have a structure to allow for two organisations to take protected disclosures from staff, then there should be some effort made to allow for better management of protected disclosures," Ms Justice Ring told Ms Daly.
She also complemented the staff from the gardaí assisting GSOC in their investigations.
Ms Ring told the committee that they now had a full complement of investigators dealing with existing and new cases.
She said for many making protected disclosures, it was a "very distressing experience" and had to be done over time.
Ms Justice Ring also acknowledged to Sinn Féin's justice spokesman Donnchadh Ó’Laoghaire that of the 36 cases in relation to protected disclosures on the books, there had not been any cases last year that led to a prosecution or recommendation of disciplinary action.
He said it seemed that most cases were carried over, and no gardaí had faced sanction arising from a GSOC investigation following on from a Section 7 disclosure.
Ms Ring said this was correct, but added they initially started with one investigator, and only now had a full complement of investigators.
She also told Mr Ó'Laoghaire that it was mandatory for the gardaí to report to them any discharge of a firearm, taser, or OC pepper spray, and while they look at them seriously and the circumstances, they did not always instigate a public interest investigation.
Deputy Ó'Laoghaire raised the case of the discharge of a firearm in a house in Cabra in Dublin.
Additional reporting Edel McAllister