Victoria Police has been criticised over its handling of criminal allegations against officers.

The Independent Broad-based Anti-Corruption Commission (IBAC) has audited 59 investigations by Victoria Police's Professional Standards Command (PSC) from 2015 and 2016, and found “deficiencies in how some of the more serious complaints about police are investigated by PSC”, commissioner Robert Redlich QC said.

“We have made clear recommendations to Victoria Police to address these gaps, all of which have been accepted.”

Ten investigations into criminal allegations made against officers were classified as “work files”, when they actually should have been classified ‘criminal complaints’.

The allegations included claims of drug use, assault and criminal association.

“Work files” need preliminary assessments before a full investigation, but are not always immediately referred to IBAC.

The report said the number of allegations against the officers and potential conflicts of interest were understates, and not identified in files 95 per cent of the time.

Another issue was that some officers in charge of internal investigations had complaint histories themselves, which could damage community trust in the outcomes of the investigation.

One case study covered a complaint made by a detective to the PSC after a police officer was named by two suspects in an espionage investigation.

“One suspect allegedly told the detective that the police officer gave him advice on how to avoid a charge,” the report said.

“The second suspect mentioned the police officer's name at trial, stating that he had visited the subject officer's house.

“Despite allegations that the police officer attempted to pervert the course of justice and was associating with criminals, no allegations were listed in the investigation report, which stated that the work file involved an intelligence probe only.”

IBAC auditors say the “criminal association” allegation should have seen it classified as a complaint of criminality not connected to duty, instead of a work file.

A total of 15 complaint files against officers should have been referred to IBAC but never were. They included allegations of rape, handling stolen goods, threats to kill and interference in an investigation.

IBAC made a series of recommendations including being notified whenever matters are classified as “work files”.

The watchdog also called on police to consider imposing new checks and criteria for recruiting officers to work in the unit, and consult the Office of Public Prosecutions when the PSC believes a reportable offence has been committed.

Victoria Police says it “acknowledges the findings” of the audit and “accepts its recommendations”.

“As acknowledged by IBAC, Victoria Police has taken recent steps that have improved its management of Conflict of Interest in complaint management and is already reviewing its complaints handling system which will acquit several of the recommendations,” it said in a statement.