Toronto's handling of the homeless during the COVID-19 pandemic has "put lives at risk," a new lawsuit alleges.

The group of organizations, which includes a drop-in centre, is seeking an immediate injunction in an effort to force the city's 75 shelters to follow physical distancing rules.

The suit, which was filed Friday in the Superior Court of Justice, alleges the city violated shelter residents' Charter of Rights and Freedoms and breached the Ontario Human Rights Code.

They allege the city's standards of placing beds 0.75 metres apart, rather than the two-metre distance health officials have mandated, and the use of bunk beds in shelters, is unconstitutional during the pandemic.

"They put lives at risk," the groups said.

"In so doing, they also disproportionately burden members of historically marginalized groups who are overrepresented in the shelter system and deprive those groups of the benefit of physical distancing measures generally available to the housed public."

The organizations said they "seek to vindicate the constitutional rights to life, security of the person and equality of Toronto's most vulnerable residents."

As of Friday, there were 135 residents in the shelter system who tested positive for COVID-19, with the majority occurring in an outbreak raging at a shelter for refugees.

Sanctuary Ministries of Toronto, Aboriginal Legal Services, Advocacy Centre for Tenants Ontario, Black Legal Action Centre, the Canadian Civil Liberties Association and HIV & AIDS Legal Clinic Ontario filed the suit.

The city said in a statement it is working tirelessly to rapidly find solutions for the most vulnerable during the pandemic.

"A critical component of prevention work has been working closely with service providers to take steps to increase physical distancing measures on site, where possible, including reducing or eliminating the use of bunk beds," the city said.

"Shelters continue to meet the increased physical distancing guidelines of two metres."

There are about 7,000 people in the city's shelter system, the most in the country. There are 75 shelters and respite centres in Toronto, 11 of which are operated by the city.

About 3,000 of those residents are already in hotels and family settings, the city said.

Advocates have been calling for reform in the notoriously overcrowded shelters for decades.

The city said it has opened 11 centres during the COVID-19 crisis as a way to reduce crowding and are also in the midst of buying or leasing hotels in an effort to give each resident a private room.

They have secured 1,200 hotel rooms thus far, the city said, and are continuing to look for more.

"Some 770 people have been moved to hotel rooms and another 492 people to community space," the city said.

The city said it has redeployed hundreds of employees to help during the effort.

"Relocating people out of a familiar shelter setting, however, is complex," the city said.

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"Respecting individual needs remains a key consideration before moving someone to a new space."

It said the "enormous effort" includes inspections and ensuring the amenities are adequate for the residents, and that it has to also secure contracts for cleaning, catering, security and laundry services.

"Implementing a comprehensive response as quickly as possible for Toronto's most vulnerable has been a city priority," the city said.