The magistrate refused bail in a children's court after hearing a number of workers had been assaulted by the boy.

She said she was "very concerned" about the attitude of MFS towards the reporting of daily incidents involving the youth.

A police officer told the hearing two workers had told her they were fearful about the future of their jobs if they made statements to police.

The magistrate said that every day workers and the community was being put at risk.

"He's dangerous," she said.

"I'm beginning to have little confidence MacKillop will report the behaviour.”

One worker said she was scared to grab the youth back for fear of losing her job.

The youth has been charged with 13 offences including unlawful imprisonment, assaults, making threats and damaging property.

He has been remanded in custody and will be held at the Parkville youth justice centre where he has previously been held in almost isolation.

​MacKillop Family Services area manager Cameron Burgess said to suggest the service had a culture of suppressing staff reporting to police was ludicrous.

"I'm ropeable. What was said in court is not reflective of the quality of service we provide," he said.

"To suggest we collude concerning criminal matters, at the risk of staff safety, is absurd.

"I can't speak highly enough of the work being done in an extremely complex case. Why would we want to create an environment where our staff are discourage ​from reporting incidents to police."

Mr Burgess said police attended at the youth's home weekly to help break down the barriers.

"We encourage staff to call police if they feel they are losing control and staff have even taken this child to police," he said.

"To suggestion there is a culture of suppression would be negligible on our part and not how we run our service.

"What is the possible motive? It's against our best interests.”

The area manager said his service had worked with the youth during the past four months and there had been no significant community safety concerns.

"That's nothing short of amazing work," Mr Burgess said.

"Yes, our staff have struggled to adapt and maker adjustments in this highly complex situation."

Mr Burgess said he expected that disgruntled staff had made complaints to police.

The youth’s behaviour involved shoving a worker into a cupboard and locking the door with a zip tie and then holding it closed with a chair.

He repeatedly threatens to rape women carers, physically assaults them by throw things and hitting them and during a trip to Melbourne was so disruptive the driver had to stop a number of times.

During a trip to Melbourne in November he yelled loud abuse and barked like a dog to distract the driver.

He threw carrot sticks, DVDs and CD, moved around the inside of a Tarago, and threatened to slit the throat of a worker and watch her bleed out.

He grabbed a woman's elbow and bit her, kicked a carer to the head and pulled her hair.

The next day he unexpectedly punched a worker to the stomach.

Earlier this month he stomped on the feet of a carer 10 times, ripped off her lanyard and grabbed her by the neck four times.

Last week a female carer was on the way to the kitchen when the youth grabbed her arm and pushed her into a cupboard when he then secured with a zip tie.

When another worker tried to intervene three times, he grabbed her and shoved her against a wall on each occasion, while threatening to rape her during a 45-minute ordeal.

The police officer said it was clear the youth's behaviour was escalating and that MFS was not reporting the daily incidents to police.

A solicitor on behalf of the youth said MFS was happy to have him back.

He said the boy had written a letter saying that he needed to be more respectful, but the solicitor admitted the behaviour was concerning and had been normalised.