Assistant Commissioner Brett Guerin ignored the recommendations of an internal police investigation when he decided not to lay the charges against the two officers, who allegedly assaulted two teenagers in 2014.

Mr Guerin, who is responsible for internal force watchdog the Professional Standards Command, also chose not to consult the OPP before he proceeded with assault charges against Leading Senior Constables Dennis Gundrill and Simon Mareangareu over an alleged altercation outside a Vermont convenience store.

According to correspondence obtained by Fairfax Media, the serious allegations of perjury and attempting to pervert the course of justice will be dealt with by an internal disciplinary hearing.

Both officers have been allowed to perform administrative duties on full pay until they face court.

The pair were investigated only when a mobile phone video of the incident was recovered.

The footage taken by one of the teenage boys was mysteriously deleted from the phone within hours of the alleged attack on Christmas morning 2014, but was later retrieved when the father of one of the teenagers paid $4000 to an IT consultant.

The father is expected to launch civil action against Victoria Police, after accusing the force of an "old-fashioned cover-up".

In a letter to the Director of Public Prosecutions, the boy's father claims Detective Senior Sergeant Ian Shepherd recommended Leading Senior Constables Gundrill and Mareangareu be charged with attempting to pervert the course of justice.

"The perpetrators are back at work, they have learned they can get away with laying false charges ... the entire criminal justice system has been compromised in a way that our laws are intended to prevent," the father said in the letter to the OPP.

The OPP has confirmed it would review the case.

A police spokeswoman said the force was unable to make any comment while the matter was before the courts.

Leading Senior Constables Gundrill and Mareangareu are due to appear in Ringwood Magistrates Court on June 3, after a mention hearing was adjourned last week.

The two 16-year-olds were originally charged with assaulting police, resisting arrest and possession of about one gram of marijuana. All charges against them were dropped last August.

An internal investigation by the Whitehorse crime investigation unit was launched when the father of the alleged victim handed over the video.

There are discrepancies between the statements given by Leading Senior Constables Gundrill and Mareangareu, which also differ from the footage of the incident and evidence given by an independent witness, a security guard.

The officers' explanations for questioning the two boys on Christmas morning also appear to have changed.

And the footage reveals one of the police officers yelling "Let's get rid of that video" as he grapples with one of the youths.

It is understood at least three senior officers involved in the internal investigation, including Senior Sergeant Shepherd, supported a decision to lay the more serious charges of perjury or perverting the course of justice but appear to have been overruled by Mr Guerin.

There have been previous concerns about the veracity of statements provided by Leading Senior Constable Gundrill in an unrelated court case.

County Court judge Chris O'Neill said he had "reservations about Mr Gundrill's credibility" during a civil trial in 2013 in which video footage appeared to contradict the officer's testimony.

"Clearly the evidence was given after a reconstruction from the footage ...That was an artificial reconstruction and not an honest reflection," Judge O'Neill said in his ruling.

The handling of the investigation into Leading Senior Constables Gundrill and Mareangareu raises further concerns about the practice of police investigating their colleagues. The Independent Broad-based Anti-corruption Commission had refused requests to examine the matter.

According to the Human Rights Law Centre, more than 90 per cent of complaints about police conduct are referred back to Victoria Police, despite IBAC having jurisdiction to handle them.

Last July, Victoria's highest court referred allegations of police brutality and racism to IBAC to determine if an independent investigation should be launched into a complaint by Ethiopian man Nassir Bare.

Mr Bare claimed officers smashed his teeth in a gutter, racially vilified him and capsicum-sprayed him when he was handcuffed, after police stopped his car in February 2009.

chouston@fairfaxmedia.com.au