Despite complaints, the Gauteng Department of Health says it is happy with the standard of facilities used to accommodate South Africans repatriated from the US on Sunday.
However, uncertainty remains over how 180 people were diverted from hotels procured by the Department of Public Works.
Health department spokesperson Kwara Kekana told News24 the Eskom, Transnet and Telkom facilities used to accommodate the group were approved by the department.
"The sites have been used for over a month now to accommodate people who are unable to quarantine and isolate at home. Additionally, the sites are used to help national efforts of repatriation, to accommodate repatriates, when the national government needs help," Kekana said.
"The Gauteng Department of Health does not determine who goes to which site with regards to repatriates. Allocation is made by the national Department of Health based on available beds in Gauteng health-operated quarantine sites."
However, Public Works Minister Patricia de Lille said the department was not informed of the diversion of 180 passengers to these government facilities.
She added it had already signed a service level agreement with two hotels to accommodate the repatriates, but were informed the next day not all of them had arrived at the hotel.
"We did the procurement, and everybody knew that national did the procurement for the two hotels. Without informing us, a decision was taken somewhere to divert 180 people to those sites," De Lille said.
"If they wanted to take some of those people to those facilities, they should have at least had the courtesy to tell us that they were taking 180 people, then we would have not procured for 245 people, but it was just done without informing the Department of Public Works."
She added the department could only get approval for sites from the national Department of Health.
For this reason, the director-general of the Department of Public Works had launched an investigation into who took the decision to divert the group, once complaints about the facilities arose.
Earlier this week, two repatriates at the Transnet facility told News24 their living conditions were unhygienic and dilapidated.
When they got to the facility, they found stains on the walls and floors, as well as on the mattresses and bedding. Mould grew in the bathrooms, which frequently flooded, while furniture and curtains were on the brink of falling apart.
They allege the food they were given was "disgusting", with "no nutritional value", and they had felt as if they were in a prison as they were not allowed outside for some sun.
However, Kekana said Health MEC Bandile Masuku had visited the sites and was satisfied with what he had found.
"A team from the office of the MEC has been to the sites and we are satisfied with the standard at these quarantine sites."
The Department of Public Works previously said the repatriates were taken to the wrong facility, with De Lille suspecting a scam.
However, Kekana said the health department was not aware of any scam.