Strathclyde Police should not have commissioned its own inspector to investigate a complaint against the force in the case of Kevin Ruddy, the Court of Session ruled this week, nine years after the original complaint.
Calum Steele, general secretary of rank-and-file body the Scottish Police Federation, told Holyrood's justice sub-committee on policing that the ruling raises questions over how Scotland's new single police force will handle similar complaints.
English forces should not investigate complaints because of "the difference in legal system and procedures" in Scotland, Police Scotland Deputy Chief Constable Neil Richardson told the committee.
Local councillors should not be allowed to scrutinise complaints because a councillor who is accused of a crime could end up assessing their own investigating officer, Mr Steele said.
But he also questioned "how much credence will be given to a police officer or a police force investigating its own even if it is under the supervision of an independent body".
Police Scotland complaints will be supervised by the new Police Investigations & Review Commissioner (PIRC), who will be charged with undertaking independent investigations into the most serious incidents involving police.
The seriousness of complaints is a matter of "subjective judgment", Mr Richardson said.
A complaint about "overzealous" handling of a situation would be "relatively minor", while an officer accepting a bribe would be "serious", he said.
Mr Steele added: "I'm not a legally qualified professional but there are potentially some difficulties ahead. I think the Ruddy judgment is massively important and it will have lots of implications for the police service. There's no point pretending it won't."