Manitoba's children's advocate is urging the province to stop lengthy solitary confinement of youth in custody after a review that found one boy was isolated for 400 straight days in a cell no bigger than a parking stall.

Daphne Penrose and provincial ombudsman Marc Cormier jointly investigated the use of solitary confinement, segregation and pepper spray in Manitoba's youth jails.

Penrose said in a 100-page report released Thursday that the province should immediately end solitary confinement longer than 24 hours for kids in custody.

She also recommended that Manitoba Justice restrict the use of punitive segregation overall and called on the province to build a facility to address trauma, mental illness and other mental impairments youth who are locked up in jail frequently live with.

"Some youth in Manitoba have been confined in solitary, denied their basic needs and refused meaningful human contact for days and weeks on end," Penrose said of the youth, called Colton in the report, who spent more than a year in isolation.

Colton was diagnosed with fetal alcohol spectrum disorder, attention deficit disorder and other cognitive issues, she said, and spent a total of more than 650 days in solitary.

Penrose called Colton's case "a clear violation of human rights, of international standards."

"What we discovered … was extremely concerning, unacceptable and must immediately change," Penrose said at a news conference.

The investigation began in 2015 after the advocate's office fielded several complaints about segregation and pepper spray in Manitoba's two youth jails: Agassiz Youth Centre and Manitoba Youth Centre.

The review found that between September 2015 and August 2016, youth corrections staff placed 167 males in solitary confinement 498 times. About 20 per cent of cases lasted for more than 15 days.

The advocate defines solitary confinement as being placed alone in a cell for more than 24 hours without meaningful human contact or mental stimulation.

Statistics Canada data shows Manitoba has the highest rate of youth incarceration in Canada with more than 80 per cent being Indigenous.

The advocate suggested use of solitary confinement and segregation is harmful to youth and hurts their chances at successful reintegration into society.

"Ultimately, (it) may increase recidivism and compromise public safety."

Penrose did find that the use of pepper spray on jailed youth declined dramatically to two instances last year from 2010's high of 46.

Staff told investigators that may be due to "alternative de-escalation methods" such as talking to youths and having patience to wait out a situation.

In a separate report, Cormier made 32 recommendations on segregation, largely focused on reviewing compliance with correctional services laws and regulations.

Gathering data was difficult as records weren't systematic or complete, he said. Corrections employees had a "systemic misunderstanding" about what documentation was required and that led to "miscollection" of information.

"Without that data collection you are making poor decisions."

Cormier suggested that jails be made to have policies that make clear that segregation can't be used as discipline. He also called for changes to require youth be informed of their rights and access to services.

Manitoba Justice has accepted his recommendations and will put them into place by March 1, Cormier's report said.

Penrose said she has not yet heard from the department.

Justice Minister Cliff Cullen said Penrose's report is still being reviewed.

He said Manitoba's segregation policies changed last year and are in line with other provinces.

"I think it is important to know that youth in segregation are there because their behaviour poses a risk to themselves, to other inmates or to staff," he said.

"Every effort is made to ensure that youth go back into general population at the earliest opportunity."

Cullen also said the use of pepper spray in youth facilities has declined over the past few years. He said it was only used twice last year.

Cullen said segregation and pepper spray are only used as a last resort but acknowledged that more changes are needed to ensure positive outcomes.

"The health, safety and security of staff and inmates at our youth correctional facilities is one our top priorities."

NDP justice critic Nahanni Fontaine said the reports are very troubling.

"All children must be kept safe, even those serving sentences," Fontaine said in a release.

"Today, the Pallister government refused to listen to the expertise of the Advocate and heed her call for better youth mental health supports. They also failed to take responsibility for the accurate and consistent reporting of these methods. Children deserve better."

Last week, the province announced a review into the connection between youth justice and child welfare.

One of the goals is to try to keep "crossover kids" out of jail. A study of admissions at the Manitoba Youth Centre in October showed about 60 per cent of youth facing charges were also involved with child-welfare services.