Victoria's anti-corruption watchdog has launched an investigation into a botched police raid that left an innocent man with serious injuries.

Key points: Victoria Police has agreed the Independent Broad-based Anti-corruption Commission should investigate the arrest

Victoria Police has agreed the Independent Broad-based Anti-corruption Commission should investigate the arrest The injured man's lawyer says IBAC should consider charges against the officers involved

The injured man's lawyer says IBAC should consider charges against the officers involved A senior officer has said he is "appalled" and has apologised on behalf of Victoria Police

Nik Dimopoulos, 47, may lose the use of his right arm as a result of the injuries he sustained while being arrested by police in Fitzroy, in Melbourne's inner north, about 2:00am on Saturday.

Mr Dimopoulos also suffered a "major injury" to his shoulder and has had bone grafts from his hip and knee.

He also has a head injury and cuts to his face.

The Independent Broad-based Anti-corruption Commission (IBAC) said police were supportive of the independent investigation.

"IBAC, Victoria's independent police oversight agency, has determined it will investigate an incident involving Victoria Police in Fitzroy that resulted in the serious injury of a civilian in the early hours of Saturday morning," IBAC said in a statement.

"IBAC performs a critical role in independently oversighting Victoria Police to ensure officers are accountable and conduct themselves in a way consistent with the community's expectations.

"Victoria Police have agreed that in the circumstances, it is appropriate that IBAC independently investigate this matter."

Officers from the force's Critical Incident Response Team, supported by the police air wing and a canine unit, were pursuing a suspect in a home invasion and carjacking case, whom they mistook for Mr Dimopoulos.

Space to play or pause, M to mute, left and right arrows to seek, up and down arrows for volume. Watch Duration: 1 minute 1 second 1 m 1 s Victoria Police Assistant Commissioner Luke Cornelius apologises for botched raid

When police broke into the garage of the building — which houses LGBT community bookshop and cafe Hares & Hyenas — Mr Dimopoulos ran from the property, fearing an anti-gay home invasion, according to a Facebook post by bookshop co-owners Rowland Thomson and Crusader Hillis.

"It's very clear to us that police stuffed this one up," Victoria Police Assistant Commissioner Luke Cornelius said at a media conference this morning.

Earlier on ABC Radio Melbourne, Assistant Commissioner Cornelius said the incident would be subject to an "independent investigation" by the force's Professional Standards Command.

The lawyer for Mr Dimopoulos, Jeremy King, described the plan for Victoria Police to run the investigation as "an absolute joke" and was supportive of a review by IBAC.

He said IBAC should consider charges against the police officers involved.

"Victorians as a community have had enough," Mr King said.

"Victorians don't trust that Victoria Police will … look at it properly, and we really need to make sure that we have a strong IBAC who can step forward," he said.

Police entered the garage of the building about 2:00am on Saturday. ( ABC News: Damian McIver )

He said his client was recovering from major surgery and faced a long recovery.

"Nik is not doing so well at the moment, to be honest," he said.

"He's had major surgery, he's recovering from that surgery and he is deeply traumatised by the incident."

'Why is there no footage?'

Mr Hillis and Mr Thomson said at no time did they hear the officers identify themselves as police.

"Waking up to 'everyone on the floor' is one thing but for sure when Nik was running out they never said 'stop, police'," Mr Thomson said.

"Nik said 'if I'd have heard the word police I would've stopped'."

Mr Hillis said his friend was "universally considered as one of the gentlest people" around and he questioned why police were not wearing body cameras.

Mr Dimopoulos is well known in the LGBT community for running gay dance parties. ( Supplied )

"Why is there no footage? Why is there no recording, why is there nothing?" he asked.

"A simple body cam on even two or three of the people would've made a huge difference to everybody's understanding and I think it would've tempered the behaviour and the way in which the police operated."

Senior officer 'appalled' by injuries

Assistant Commissioner Cornelius said he was "appalled" by the extent of Mr Dimopoulos's injuries, "and on behalf of Victoria Police I'm very deeply sorry".

He said claims from eyewitnesses that the arresting officers had not identified themselves as police would form part of the investigation.

"From my perspective, it's entirely understandable, that someone who believes they're being the subject of a home invasion and potentially a homophobic attack, it's entirely understandable that an individual in that situation would be first and foremost focused on their safety, absolutely focused on trying to get away from that threat, and in those circumstances we know that in a dynamic situation, individuals may or may not hear what was said to them," he said.

Assistant Commissioner Cornelius said Professional Standards Command investigators had spoken to Mr Dimopoulos yesterday.

Assistant Commissioner Cornelius said he had spoken to Victoria's Commissioner for Gender and Sexuality, Ro Allen, and would visit Mr Thomson and Mr Hillis to personally apologise for the incident.

Nik Dimopoulos has undergone surgery on his arm. ( Supplied )

He said the officers involved were entitled to procedural fairness, and no decisions had been made about suspending officers while the investigation took place.

These decisions were for Assistant Commissioner Russell Barrett, who was responsible for Professional Standards Command, he said.

Assistant Commissioner Cornelius said any information from members of the public about the incident would be taken seriously, and people could also approach IBAC directly.

A Victorian parliamentary committee last year found the system for investigating police misconduct was "extraordinarily complex and confusing" and based on an "intricate, overlapping and sometimes fraying patchwork of laws, policies and processes".

It called for a police corruption and misconduct division to be created within IBAC.