The owner of the St-Édouard Zoo in Quebec faces two counts of cruelty and neglect covering over 100 animals at the zoo.
They include lions, tigers, zebras, bears, wolves, kangaroos and primates.
Authorities say their relocation to other facilities is expected to take “a number of weeks”.
The Montreal SPCA were following up on a complaint from the public when it launched an investigation into the zoo after a visit to the facility last August.
Animal protection officers found “several significant problems regarding the physical state of the animals and their living conditions” and “seized two alpacas in particularly poor condition”.
They also found the carcasses of four animals, including two tigers.
The zoo owner, Norman Trahan, was charged on Tuesday and faces up to five years in jail and a lifetime ban on owning an animal if found guilty.
The SPCA said it believes this is the first time in Canada a zoo owner has been charged with criminal animal cruelty.
The raid came just days before the zoo, about 100km (62 miles) northeast of Montreal, was to open for the season. The facility has been operating for about 30 years, according to its website.
The SPCA and Humane Society International, which has experience with mass animal rescue operations, have set up an onsite facility to assess the current health of all the animals and see which ones might need urgent care, as well as to document their living conditions.
The organisations will also be in contact with “a network shelters and sanctuaries” that can care for the animals that will be removed from the premises.