Police arrived without warning at a youth rehabilitation event co-run by the Aboriginal Legal Service of WA with five cars, arresting three boys participating in the program on Thursday.
ALS WA chief executive Wayne Nannup told National Indigenous Times the incident was "completely unforgiveable".
"We have a program with partners called Old Ways New Ways. Our partners are Hope Community Services, Wadjak Northside, and the Stephen Michael Foundation. The program is set up, and we're running a pilot right now for youth diversionary engagement; it could be community referrals, or it can come from the courts," he said.
"It's a grant that's been funded by justice reinvestment, which is now being closely looked at by the Attorney General office federally. This morning, part of our pilot, we had 20 kids roll up, which has been the most we've had, and we've only started it three weeks ago.
"We're able to engage young kids to on the on the cusp of entering the justice system, or are already in the justice system. What happened? What happened today, this morning was they had all these kids together at Wadjak Northside's offices in Balga, and the cops turned up with five car loads of cops then proceeded to arrest three young boys that are in that program, handcuff them in front of all the other kids."
Mr Nannup said the incident left all of the children present "distraught".
"We are trying to get this off the ground, providing alternatives to send for sentencing and just general youth engagement in the community. My kids are upset. My staff are upset, and it's just completely unforgivable," he said.
"It's an incredible thing that we're doing, because we're getting community referrals from all the agencies in that area, and they're so happy… This is the program. We know this thing's going to work, and it started to work already… But what happens? We give the hope to these kids, we get them there, and we show them a different way, and then you have this turn up, and we go back 200 years."
Western Australia has the highest rate of Indigenous youth over-incarceration in Australia.
WA Police said detectives from the Rapid Apprehension Squad "attended an address in Balga, making inquiries in relation to series of aggravated burglary and stealing incidents that occurred between 27 October and 3 November 2024".
The spokesperson said three 16-year-old boys were arrested at the address and subsequently charged with a combined 20 offences between them.
"Body Worn Camera vision of the arrests has been reviewed and it is clear officers acted in a calm and professional manner. All interactions appear respectful and the arrests were actioned without incident. No formal complaint has been received in relation to this incident," the spokesperson said.