A 45-year-old man is expected to appear in the Johannesburg magistrate's court after he was found allegedly operating an illegal medical centre in Hillbrow.
He was also allegedly dispensing medicine belonging to the SA and Zimbabwean governments.
The Democratic Republic of Congo national allegedly also dispensed ARVs and birth control medication stolen from public health facilities.
A raid by the national crime intelligence unit and the police, together with officials from the South African Health Products Regulatory Authority, was carried out on the surgery in Pretoria Street on Tuesday found dozens of medications and medical supplies which were ultimately confiscated.
The majority of medication dispensed at the centre were ARVs and contraceptives.
A 20-litre bucket filled with used needles, ultra-sound machines and other medical equipment were found at the facility.
The facility displays the name PT Masengo Medical and Dental Centre on the outside, but the sick notes issued bear the name of Dr William Magaila and Partners.
Dozens of medical aid claims, invoices, sick notes and completed notice of death documents were confiscated by police.
Police spokesperson Sgt Mduduzi Zondo said police received complaints from "patients" who had visited the doctor.
"Several patients who used his services came to us and reported that they were suspicious of the doctor and wanted to know if he was registered.
"We then set up an operation that started two weeks ago. When we requested his [educational] documents, [he] said they were lost," Zondo said.
The man was charged with contravention of the Health Professions Act and fraud as he could not produce documents to prove that he was a qualified doctor.
He charged patients, mostly women, R300 for consultation.
Patients continued to walk into the centre during the raid and were shocked to find the doctor in handcuffs.
"I am shocked. I have been coming here for my [contraceptives] injection since 2017," said one woman.
A 2018 report by the City of Johannesburg found that medication and medical supplies were being stolen from clinics and sold to spaza shops and nyaope rings across the city.
According to the report, medication is stolen from public clinics and sold to spaza shops owned by foreign nationals in suburban areas of Johannesburg and the townships, organised nyaope rings, GP networks and international trade (bulk supply).
According to the report, the medication was also sold to school children who create a concoction of Stilpane, Red Bull and anti-depressants.
Stolen medication and supplies include ARVs, family planning medication (tablets and injection), scheduled drugs, bandages and drips.