An Indigenous leader in Western Australia claims at-risk children were left "traumatised" after police arrested three teenage boys while they were attending a program designed to keep them out of trouble.

Detectives attended the Wadjak Northside Aboriginal Community Centre in Perth's northern suburbs on Thursday and arrested three 16-year-old boys, charging them with a string of offences.

Aboriginal Legal Service of WA (ALSWA) chief executive Wayne Nannup claimed the arrests happened in front of children attending a session of a federal government-funded program aimed at steering kids away from the criminal justice system.

Mr Nannup told the ABC up to a dozen police officers arrived at the Old Ways New Ways meeting to arrest the three boys.

He said the incident was "disturbing" and had distressed and traumatised other participants and staff who were present.

"For me it's just completely unacceptable on all levels, when we are trying to put together a program that's going to assist community and take kids away from the [justice] system and we have to deal with this, it's just unbelievable," he said.

Mr Nannup said police could have approached the matter in a different way.

"It takes a lot of work to get these kids' trust and now we've got to take three, four steps back again," he said.

Boys charged with burglary

WA Police said on Friday morning they had charged three boys with a total of 20 offences following an investigation into burglaries across Perth in the past two months.

Two of the boys were charged with aggravated burglary and stealing a motor vehicle, and the third was charged with attempted aggravated home burglary.

Police would not say how many officers attended, but said body-worn camera footage of the incident had been reviewed and "it is clear officers acted in a calm and professional manner".

"No formal complaint has been received in relation to this incident."

Mr Nannup said despite the alleged offences, the arrest of the boys at the meeting was not the time or place.

"Some of the other young boys in the program were visibly distressed," he said.

"That is their experience now — they will just think of their peers or their brother-boys being put in handcuffs.

"They have to feel safe to come into our program and we felt that was significantly disrupted.

"This program has received a setback, but we will keep focusing on it. Our young kids need it."

Boy released from custody

One of the boys charged appeared in the Perth Children's Court on Friday, and was granted bail after pleading guilty to several aggravated burglary and stealing offences.

The court heard the 16-year-old from Ballajura had been attending the Old Ways New Ways program for the past three weeks and was "doing well".

Magistrate Stephen Vose told the court in considering whether to release him from custody, he had to weigh up the need to protect the public with the potential benefits of the boy remaining on the program.

"If someone is making an effort, albeit a belated effort, that counts a huge amount to me.

"There's always hope, people can and do change … you've made some steps in the right direction."

As well as the boy's progress with the program, Magistrate Vose said he also took into consideration that the offences did not involve violence.

He instructed the boy to continue with the diversion program and resist the peer pressure to reoffend.

"If there are people in your life that drag you down … you're going to have to keep your distance," he said.

'Not an ideal situation'

WA Premier Roger Cook said he has asked for more information on what happened.

"My understanding is that [police] were unaware of the circumstances of those people who gathered there but I'll continue to investigate further and just find out what's gone on here," he said.

"My concern is for those young people who were participating in that program.

"These programs are important, because we know diversion works … and we know if we can get young people on a better pathway they won't come into continuous contact with our justice system.

"It's not an ideal situation."

The Old Ways New Ways program is described on its website as "an alternative model to youth diversion to help turn the tide on youth detention".

It would "wrap around the young person and their family within a central hub environment, providing innovative, evidence-based and culturally safe services that will support young people and lead them on a healing pathway away from the criminal justice system".