The government could be forced to deport foreign nationals who remain in the country illegally after the closure of the temporary shelters, the Department of Home Affairs has said.
The camps were closed at the end of last month. The deadline for the closure of the camps was extended to September 30 by the constitutional court after an application by advocacy groups.
"The department does not have the infrastructure to accommodate those who do not want to be reintegrated," Home Affairs spokesman Siobhan McCarthy said.
McCarthy said the department would have to decide whether to wait until the six-month grace period provided by exemption certificates expired in December or to deport the nationals after the closure deadline.
He said the department was waiting for directives from Home Affairs Minister Nosiviwe MapisaNqakula on how to deal with illegal immigrants with exemption certificates.
The certificates were awarded at the shelters and exempted them from arrest and deportation. The certificates also gave them a grace period of six months to apply for legal documentation.
Three shelters remain open after the closure of the camps in Midrand, Corlett Gardens and Springs, said provincial government spokesman Thabo Masebe.
Foreign nationals at the Glenanda shelter, south of Johannesburg, said reintegration would be impossible without alternative accommodation and jobs.
Masebe said "less than 2000" immigrants remained at the shelters. The drop in numbers signified that reintegration was taking place.