Without the file, detectives are unable to investigate further because it holds the victim's statement, contact details and nature of the complaint. In this case, it is understood several victims were not contacted by detectives after laying a complaint.
Police would not tell the Herald on Sunday how many cases had been stalled or for how long.
Auckland City district commander, Superintendent Richard Chambers, was confident victims had not been let down.
"I am reassured that our own internal processes identified an apparent issue and I am confident that services to victims has not been compromised," he said.
The police source said the files were only discovered after a detective who was assigned a case couldn't find the physical file and reported it to top brass.
It is understood the officer said he had "forgotten" about the files after he put them in a cupboard.
Chambers confirmed the investigation was under way and said it was being taken seriously.
"My decision to stand the member down came as a result of police internal processes identifying some apparent inconsistencies in accepted practice," he said.
"The matter was appropriately dealt with immediately and my subsequent action demonstrates how seriously I view it."
Police have made victim-focused policing a priority in the wake of the Roastbusters investigation where they were slammed for numerous failings.
On Thursday, Commissioner Mike Bush said "the focus of modern New Zealand Police is putting the victims at the heart of what we do and taking a preventive approach to offending".
