The Canberra Times first reported Melbourne man Hamid Sotounzadeh was arrested by Protective Service Officers outside the embassy on Thursday morning.

Footage of the incident shows Mr Sotounzadeh in a heated exchange with an AFP officer before being pushed down. He is later seen lying on the ground.

Mr Sotounzadeh told The Canberra Times he could not breathe, lost consciousness and was being kicked during his arrest.

He was later released and taken to Canberra Hospital, where he currently remains with several fractures in his ribcage, neck and back.

In a statement on Thursday a spokesperson for the AFP said: "The person behaved in an aggressive manner towards the AFP members and was arrested for failing to comply with a lawful direction.

"The person was handcuffed for a brief period of time, however complained of back pain. The handcuffs were removed to ensure the health and wellbeing of the person."

In an updated statement, an AFP spokesperson confirmed on Friday the arrest had been referred to the internal integrity unit for investigation.

"The AFP is aware of media reporting in relation to a man who was detained for short period of time outside of the Iranian Embassy yesterday," the spokesperson said.

"The AFP is aware the man has alerted the media that he has sustained injuries during his arrest.

"The AFP is seeking to ascertain the veracity of those claims and has referred the incident to the AFP's internal integrity unit, Professional Standards, for investigation.

"The AFP acknowledges the right to peaceful protest but will take action when individuals put themselves or others in danger, break the law or fail to follow the direction of police."

Greens Justice spokesperson David Shoebridge said an "urgent independent investigation" should be launched into the incident after witnessing footage of the incident.

"I have seen the peaceful, creative nature of the political protests by the Australian Iranian community over these past months and it is extremely hard to see what could have possibly justified this violent arrest," Senator Shoebridge told The Canberra Times on Thursday.

"What makes this incident even more troubling is that the Australian Iranian community is protesting appalling state violence in Iran and are met by violent police action on the streets of Canberra."