The professional standards command, the police department that investigates internal complaints, has referred more internal investigations back to country police stations, several officers told Fairfax Media.

"You're investigating, very seriously, members that you're going to have to be working with next week. It creates an absolute nightmare," one officer said.

Police sources said cuts to the professional standards command were responsible for officers increasingly having to investigate their own.

A high-profile drink-driving case from Bendigo, where several officers were implicated in the cover-up of a colleague's drunken car crash in 2011, was investigated by an officer from the station's own forensic unit.

Though the Office of Police Integrity and the Independent Broad-Based Anti-Corruption Commission oversaw the investigation, Fairfax Media was told the local officer was the informant in the investigation and was forced to relocate because of the acrimony caused by the case.

"This bloke felt like he was handed a poisoned chalice. The conflict it created was unbelievable," a source said.

In Shepparton, police charged with assault, willful and obscene exposure and aiding the breach of an intervention order were investigated by colleagues from the same station. Similar situations have occurred  in Lakes Entrance, Mildura and Ballarat.

Fairfax Media spoke to police who have been forced to investigate colleagues and who have been the subject of investigation who said it "destroyed relationships".

Police Association secretary Ron Iddles said police should not investigate their colleagues for internal criminal allegations.

"Other than instances where there are minor management or performance issues, investigations of a serious nature, including criminal matters, should be conducted by the professional standards command," Detective Senior Sergeant Iddles said.

"To take senior managers away from their core operational responsibilities to conduct such investigations is not ideal and should only occur as a last resort if there are no alternative options available."

Federation of Community Legal Centres senior policy adviser Michelle McDonnell said the method was not transparent or independent.

"People are going through an internal police complaints process that's inherently conflicted," Ms McDonnell said.

She said even if the professional standards department investigated, it was not independent because the unit consists of police, and IBAC, the independent watchdog, was handing investigations back to the force.

"To date, IBAC have been referring a number of complaints back to police and we don't believe that process is really ensuring the community gets an independent review of police," she said.

A Victoria Police spokeswoman said there are a number of factors that professional standards police take into account when determining who investigates internal criminal allegations.

"Those factors include the seriousness of the allegation, the availability of an independent member to conduct the investigation and the amount of time it may take to resolve the complaint," the spokeswoman said.

She said that usually an investigator from a different station was assigned when an investigation was conducted at a regional level.

"If this is not possible, an investigator who does not have direct line control [supervision] of the member is assigned," she said.

She said there had been no recent cuts to the professional standards command.