The couple running it told officials they were housing 60 people, but upon inspection, more than three times that number were found, including more than 30 women.
The group, mostly believed to be drug addicts, were found in crowded rooms and without access to functioning bathrooms or running water.
“Some [of them had] been at the alleged illegal centre for a while,” the department said.
Gift Skhosana, one of those held at the facility, told local broadcaster Newzroom Afrika it was “common practice” for patients to be chained.
“They chain us as punishment [and] when you gain entry,” he said.
Despite this, Skhosana, who was a drug user, said the facility helped him get clean and overcome his addiction.
Another person, who was not named, said his experience with the facility left him needing help mentally.
The couple charged a monthly fee of 3,000 rand ($182; £137) to house the patients, of which almost a half would go to the church.
Fourteen of those found at the centre have since been taken to hospital for further medical treatment, police said.
Officials said 132 have been reunited with their families.
The couple is expected to appear in a local court on Monday.