Dozens of children who are Canadian citizens have been held in immigration detention centres in conditions that can cause physical and psychological harm, according to a new report.

The study, called "Invisible Citizens: Canadian Children in Immigration Detention," was produced by the International Human Rights Program at the University of Toronto's faculty of law and released today during a news conference on Parliament Hill.

It found the best interests of the children were not adequately accounted for at the time of the arrest and detention of the mothers, and that the fundamental rights of the children were violated.

The report calls on the government to find better alternatives, including community housing, and warns that Canada's international reputation is at stake.

"If Canadian authorities do not move quickly to address the serious human rights violations of some of the most vulnerable members of our society, and entrench the initial progress of the past year into law and practice, Canada's government will further undermine its reputation as a human rights defender," the report reads.

Program director Samer Muscati welcomed the government's recent commitment to reform the detention regime, but called for fast action on the plan and for more public data to be released.

"These are good signs, but the federal government must move urgently to implement viable alternatives to detention and family separation," he said.

"In cases where unconditional release is inappropriate, families should be accommodated in community-based programs that involve, for example, reporting obligations, national deposits and guarantors."

In a foreword to the report, Audrey Macklin, chair in human rights law at the University of Toronto, said some of the minors detained were infants and toddlers, while others were attending school until they were "torn away from the life they had known and shunted into detention."

Their parents, usually mothers, had to choose between giving up their children to child protection authorities or bringing them into detention with them.

"When it comes to children, migrant detention isn't just for migrants," she wrote. "Children with Canadian citizenship are also locked up."

The program interviewed nine detained and formerly detained mothers of Canadian children from the Middle East, West Africa, Central America and the Caribbean. They described conditions in Toronto and Laval, Que., centres that hampered their ability to properly protect and care for their children.

"Without exception, the mothers expressed deep anguish about the detrimental consequences of the experience on their children's health," the report reads. "Their children had difficulty sleeping, lost their appetite for food and interest in play, and developed symptoms of depression and separation anxiety, as well as a variety of physical symptoms. Many of these symptoms persisted after release from detention."

Through access to information requests, the program found that for each year between 2011 and 2015, there was an average of at least 48 Canadian children staying at the Toronto Immigration Holding Centre for some period of time as "de facto detainees."

The report says this is an underestimate of the total number of Canadian children housed in immigration detention, as the authors were only able to extract data from the Toronto Immigration Holding Centre.

More recent figures suggest the number of Canadian children housed in detention has dropped significantly over the past year, but the report says the frequency of families being separated has not followed a similar trend.

"Children who are spared detention but are separated from their detained parents experience similarly grave consequences for their mental health," the report says.

The report says Canadian children living in detention are by and large an "invisible population," because minors are considered "guests" of the CBSA and not counted as a legal category. That means their interests are not taken into account in the decision-making around their parents.

The report also said the federal government has resisted gathering and disclosing data on the number of children in detention because they aren't legally counted as "detained," but noted recent steps to improve both conditions and transparency.

NDP immigration critic Jenny Kwan called the report "shocking" and said Canada is breaching international law and charter rights.

"This is a disgrace," she said during question period in the House. "Will this government finally amend the Immigration and Refugee Protection Act and prohibit the detention of children?"

Public Safety Minister Ralph Goodale said immigration detention is a measure of "absolute last resort" and that the government is investing in new ways to improve the system and to minimize its use.

"We want to avoid the housing of minors in detention and facilities as much as humanly possible," he said, noting the report said signs of improvement are already underway.

Last year, Goodale announced the government would spend $138 million to upgrade immigration detention centres across Canada, and said the objective is to make detention a last resort.

The government also promised to consult with stakeholders to find ways to minimize the number of minors in detention.

Immigration detention facilities in Vancouver and Laval, Que., are also set to be replaced.

The government's other reform objectives include reducing the use of provincial jails for immigration detention, improving physical and mental health care to detainees, and increasing transparency.