Police are investigating an official complaint about the treatment of one of the five men arrested in Saturday's counterterrorism raids in Melbourne.

Two men remain in custody after the early morning raids, which were sparked by what police allege was a plot to target police at Melbourne's Anzac Day events.

Sevdet Besim, 18, of Hallam, has been charged with conspiring to commit a terrorist act. Another man is being held under a Preventative Detention Order (PDO) which allows him to be held for 14 days – the first time such an order has been used in Victoria.

Three other men have been released, with one of them expected to be charged on summons with weapons offences.

Families of two of the five men arrested have alleged police used unnecessary force and assaulted the men who were taken in for questioning.

One of the men has lodged an official complaint.

Victoria Police issued a statement which said it had received a complaint regarding one of the men arrested, which had been referred to its Professional Standards Command.

Sorry, this video has expired Police investigate mistreatment claims during terror raids

Acting Assistant Commissioner Tim Cartwright said he had "seen and heard" the complaints.

"We will certainly investigate them," he said.

"These are raids carried out in high-risk situations, 3:30 in the morning, we believe at least some of these people will be armed and will have a strong motivation to hurt police.

"I'm not surprised there are some minor injuries as a result."

Man's behaviour improved with Islamic study, father says

The father of one of the men who was arrested has told the ABC his son's behaviour improved after he began attending the Al Furqan Islamic study centre in South Dandenong, which was also attended by Abdul Numan Haidar, who was shot dead after stabbing two police officers last year.

The man told the ABC his son had been interviewed by police after Haidar's death.

Sevdet Besim posing in a forest in a photo on Instagram (date unknown) ( Instagram )

But he said the family had seen a change in their son's behaviour after he began attending Al Furqan last year.

"Before he started to pray, [he] was in the house aggressive, he broke [things], like a child. But after when he started to pray he really changed behaviour, 100 per cent," he said.

"Now he was very good, always. Never, never yells, never, never do bad in house.

"He's always nice talking when I see him, but I [do] not see him very much."

Assistant Commissioner Cartwright said all the young men arrested were associated with Al Furqan and Haidar at some stage.

"Association is what we are seeing. It doesn't mean Al Furqan, or doesn't say anything about what Al Furqan has had to do with their radicalisation, if we can call it that, but we will continue to investigate," he said.

"We want to find out what's led these young men to the state we are seeing now, what's radicalised them to the point they want to carry out these acts."

The father said the family was traumatised when police broke into their home in the early morning hours.

He said he had a gun held to his head and was forced to lie on the floor for 30 minutes.

He said police told him: "One more word I kill you. Doesn't matter for your kids."

"My wife she starts screaming. Police call ambulance to come and help her... I notice everything in the house is broken, the door, everything."

Police said three of the arrested men were injured in the raids, and the father said his son's arm was broken.

"I was in shock yesterday. I just cry all day because when I remember his face ... when I came into his bedroom. It's very hard," he said.

Another of the arrested men said he did not resist arrest and was covered in blood after being attacked by police.

"After my hands were cuffed, laying on my stomach, I got kicked in the head," he said.

"Then he [one of the police officers] grabbed me, slams me into the fridge, as you can see there'll be blood on the fridge.

"Then [he] slammed me on the ground and then hit me with his gun and I think I passed out then."

Interim Preventative Detention Order in place

Assistant Commissioner Cartwright said police were assessing how long the man would need to held under the PDO, as the investigation progressed.

"This is an interim order so it does not run through for the 14 days at this stage," he said.

"It can run for 14 days, that's the extent of it."

He said police were holding the man while they tried to determine whether there was enough evidence to charge him.

"One of the things we are trying to determine [is], what – if any – offences have occurred, and then if there is sufficient evidence to charge the person," he said.

"The raids the other morning were just part of the investigation, so the investigation doesn't stop just because we have done those raids.

"As with all these people, as you'd expect, we will continue the investigation until there is a court hearing."

Assistant Commissioner Cartwright said he understood that the man in detention had been able to contact a lawyer, but he was not aware if the lawyer had met with him.

"One of the requirements of the legislation of the order is we are not able to interview the person," he said.

"We have had to appoint an independent superintendent to make sure his rights are maintained, so that's occurred."