TORONTO -- A review of nearly 1,300 child welfare cases spanning 25 years has found that a now-discredited hair analysis program in Toronto that tested for drug and alcohol use caused extensive -- and potentially irreversible -- harm to vulnerable families across Ontario.

An independent commission tasked with examining the Motherisk hair-testing program said Monday the child welfare system's reliance on the analysis was "manifestly unfair and harmful" even when it did not substantially affect the outcome of cases.

The commission led by retired provincial court judge Judith Beaman said the tests were used to determine parents' credibility and investigate suspicions of substance use. The results were given excessive weight by the organizations and the courts, Beaman said.

"The testing was imposed on parents and other caregivers who were among the poorest and most vulnerable members of our society. There was scant regard for due process or their rights to privacy and bodily integrity," she said in a news conference.

"Most of the parents who were tested were powerless to resist. They told us they submitted to the testing under duress, in fear of losing custody of or access to their children. In some of the cases we reviewed, parents were told explicitly that this would be the consequence if they did not submit to testing."

The tests had a significant impact on the outcome of 56 cases and seven of those families have obtained legal remedies, with four cases involving children being returned to their parents' care, Beaman said.

But for many families, the damage cannot be undone, she said, noting the courts may decide it is not in a child's best interest to go through another upheaval.

"The decisions we make in child protection are often devastating and irrevocable," she said. "That is why it is critical that only reliable evidence and a fair process be used in the service of making those decisions."

The commission was convened two years ago after another report found the Motherisk program run by Toronto's Hospital for Sick Children fell short of international forensic standards for use in child protection and criminal proceedings, and said the lab "frequently misinterpreted" test results.

Children's aid societies were directed in 2015 to stop using the Motherisk tests and the hospital shut down the program after apologizing for the issues.

But the tests had already been used in thousands of child-protection and criminal cases, and the program came under scrutiny after an appeal court decision highlighted differing expert opinions about a particular hair-testing method previously used by Motherisk.

"The discovery that unreliable test results were used as part of expert evidence in child protection proceedings for so many years undermines the public's confidence in the fairness of our justice system, particularly with respect to how it treats vulnerable people," Beaman said in the report.

Children's aid societies and courts often drew negative inferences about parents who didn't submit to testing or who disputed the results, she said. The tests were often used as a proxy for assessing parenting and the results were regularly admitted into evidence without the usual checks and balances, she said.

Beaman raised similar concerns about urine tests she said are currently being used to screen for alcohol and drug use in child protection cases.

The Motherisk saga has shown that child protection and court systems must be more careful in how they use expert evidence, and that more supports are needed for families and communities, particularly Indigenous and racialized communities, she said.

The commissioner issued 32 recommendations, including changes to legislation on the use of expert evidence, more education for judges, more funding for band representatives in First Nations, the creation of family-inclusive substance abuse treatment programs and measures to address racism in the child welfare system.

She also recommended extending free counselling services to the affected families for three years on top of the two they have already been offered.

The provincial government has accepted the recommendations and promised to continue the counselling, as well as form a taskforce on the issue, with a progress update due in a year.

"What we're seeing today is a long legacy of the way the system has been built. There's been some systemic issues that have been at play and, I believe, systemic racism at play when we talk about communities like Indigenous communities and the black community," said Michael Coteau, Ontario's minister of children and youth services.

The minister said the province has already taken steps to address many of the issues by passing new child welfare legislation last year that puts children at the centre of decision-making about their care.

Asked about the use of drug tests in child welfare cases, Coteau said there is no standard process at the moment but agencies must make sure to consider a variety of factors.

The review looked at cases between 1990 and 2015 involving Motherisk and in which children were permanently removed from their families.