Police Scotland has failed to refer allegations that its officers committed crimes to prosecutors, Holyrood's justice committee has been told.
Criminal allegations against serving police officers should be passed to the Crown Office for investigation.
However, MSPs heard claims this did not always happen.
In one incident someone being "unlawfully detained" by officers was said to have been treated as a "quality of service complaint".
The Police Investigations and Review Commissioner (Pirc) claimed the example was one of several where Police Scotland had "failed to refer criminal allegations against officers to the Crown Office and Procurator Fiscal Service as required".
For non-crime classifications, the force can investigate the allegation itself without having to pass it on.
Punched in the face
The Pirc commissioner, Kate Frame, told the justice committee that "incompetence" or "more sinister factors" could be responsible for the police failures, which meant that the Crown Office was unable to pass the cases to Pirc for an independent investigation to be carried out.
Police Scotland has strongly denied Ms Frame's claims, with Assistant Chief Constable Alan Speirs insisting: "The assessment of criminality is subjective and undertaken in accordance with the Lord Advocate's Guidelines.
"Police Scotland categorically rejects the assertion made by the commissioner that any failure to report matters is due to 'sinister aspects'."
During the committee meeting, Ms Frame highlighted a number of cases, including an allegation of someone being punched twice in the face by an officer being recorded as "excessive force" instead of assault.
Ms Frame also claimed that: "There is another example of an allegation of rape, that was recorded as incivility."
However, Pirc later clarified that: "What the commissioner was referring to was that in the course of an alleged rape investigation a complaint was made against a serving police officer which was categorised by Police Scotland as 'incivility'.
"After the Pirc's intervention, the matter was reported by Police Scotland to the Crown Office and Procurator Fiscal Service (COPFS) as an 'attempt to pervert the course of justice' by a serving police officer."
The commissioner said she had only found out about the cases because the complainers were unhappy with the way the police investigations were carried out, and had approached Pirc to ask for a complaint handling review.
Ms Frame said: "At that stage we were able to refer the matter to the Crown Office for their instructions in relations to the criminality involved.
"Had the complainers not had the option of coming through the complaint handling process we would have been none the wiser."
She also said she was concerned about the "level of police discretion which continues to allow them to investigate some of their own actions".
Ms Frame added: "I think there is maybe a combination of factors that have contributed to it, either by the way of incompetence or other more sinister aspects."
But she told the committee it was "very difficult to assess" how widespread the issue was, because she only finds out about "the complainers who come to us after the event, and some may very well not".
'Fair and rigorous'
Police Scotland said it deals with more than 6,000 complaints annually, and that all complaints against the police are fully recorded and "subject to fair and rigorous investigation".
ACC Spiers said: "Every complainer has a right of recourse in circumstances where they are dissatisfied, and are provided by Police Scotland with details of how to seek further action.
"It is notable that only 5% of complainers seek these further steps through Pirc.
"Incidents are referred to Pirc in line with current legislative requirements and over the last year 421 matters were referred to Pirc with 36 of them investigated.
"This demonstrates a commitment to a high level of transparency whereby over 90% of matters referred are not subject of further investigation by Pirc."