Two boys aged 16 and 17 are planning legal action against the government for long periods of "solitary confinement" endured in the past two months, which they say led them to self-harm and attempted suicide.

Last week, Mr Elliott called for an independent review "to identify ways to move away from lengthy periods of time in rooms."

On Friday, he said "the practice of routine extended times in rooms" had stopped but he could not say when.

A senior Juvenile Justice source said it had only stopped using lengthy isolations "very, very recently." Another source who works with detainees said the practice had resumed after a relaxation of conditions last week.

Fairfax Media has been now made aware of five boys at the Sydney jail Cobham who were locked alone in their rooms for 23 hours a day for 10 days or more in recent months.

The boys, each charged with or convicted of serious offences, spent their "recreation" hours handcuffed in small enclosures and had no contact with their peers. It is understood isolated detainees often engage in self-harm, such as banging their heads against walls.

In September, Mr Elliott told a parliamentary budget estimates hearing "there is no provision or practice of isolation of young people in custody."

"That was the best information I had at the time," he said on Friday when asked if he had misled parliament.

"Because I am not confident that that may be correct, I've asked the Inspector of Custodial Services Fiona Rafter to both investigate what's best practice and what we should be doing."

Mr Elliott announced an overhaul of Juvenile Justice's governance, record keeping and behaviour strategies as well as $1 million to train staff dealing with high-risk detainees.

He confirmed one boy spent 166 days in a 10 month period isolated in the "most restrictive" phase of the Chisholm Behaviour Program, designed to manage high-risk detainees transferring to the Cobham centre from another jail.

The program was closed in May following a slew of complaints from lawyers and youth advocates to the Ombudsman, who chose not to formally investigate.

Mr Elliott said detainees were kept in their rooms for long periods in the program because of their "complex needs and misbehaviour."

A Juvenile Justice spokesman last week said no isolation took place in its centres because children could always use intercoms to contact staff, arrange appointments with health workers and chaplains or complain to the Ombudsman.

A senior Juvenile Justice employee said some staff had deliberately hidden the practice of isolation by manipulating statistics.

The source said there had been a "push back" by some staff wishing to keep the power to lock detainees on their own in their rooms for long periods.

Last weekend, three detainees allegedly assaulted a 56-year-old female guard at the Cobham centre after requesting she find them ping pong balls.

Julie Bond, a senior industrial advocate with the Public Service Association union, said her members wanted the re-establishment of a specialist unit to deal with high-risk detainees.

Ms Bond said a new unit for these detainees would ensure that "if there is an assault on a member of staff they are not just locked away for a few hours, there are proper consequences".

Rebecca Dunlop, the lawyer representing the two boys preparing to sue the government, has begun subpoenaing documents.

The minister said he expected the results of the independent review in January.

Do you know more? Email patrick.begley@fairfaxmedia.com.au or jmaley@fairfaxmedia.com.au

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