Patients and nurses particularly in the Eastern Cape, Gauteng and Mpumalanga continue to report medicine stock-outs at local clinics, including shortages of antiretroviral medicine.
This is despite repeated assurances by some provincial health officials that there are no such stock-outs.
Last Friday, over 50 patients held a sit-in protest at the Village Clinic in Lusikisiki in the Eastern Cape after being told that the ARV efavirenz was out of stock. The clinic also did not have the new three-in-one ARV, Tenofovir-emtricitabine-efavirenz.
Meanwhile, patients throughout Gauteng have reported a province-wide shortage of the ARV lamivudine (also known as 3TC) and, to a lesser extent, tenofovir.
In Ekurhuleni, clinics affected by the lamivudine and tenofovir stock-outs include Phenduka, Dresser, Sonto Thobela, Tsakane Main, Andries Raditsela and Chris Hani clinics as well as Moyo andTembisa Health Care Centres.
Peggy Dlamini, a patient at Phillip Moyo, said she has been dismissed from work due to being absent from work every Thursday, trying to get her treatment.
"I spent almost three weeks missing a day of work to come get my treatment, but I was always going home empty handed and now I have been laid off at work," says Dlamini.
Portia Serote who works for Treatment Action Campaign, said depot authorities had told them they lacked space to store drugs.
Provincial spokesperson Chris Maxon blamed the shortage on "supplier capacity challenges".
Gauteng Health MEC Hope Papo reportedly visited Daveyton clinics late last week to check on the situation.
HIV doctors are concerned that disruptions to their patients' ARV treatment could increase the cases of drug-resistant HIV, as is the case with tuberculosis.
Tuberculosis medication is also running short in some Tshwane and the Eastern Cape clinics, while some clinics don't have insulin for diabetics, or medicine to treat epilepsy or asthma, according to reports from OurHealth monitors visiting local clinics.
Stocks of the tetanus vaccine, used to protect against infection, are also reportedly very low countrywide.
"We are concerned about reports of the stockouts, particularly of ARVs, and an instruction has been issued that buffer stock is sent to facilities reporting shortages," said national health department spokesperson Joe Maila.
Maila added that the national department was trying to ascertain "who has what, where and why".
"People can't say they don't have stockouts because they have medicines at the depots while the facilities are saying they don't have stock, so we are conducting an exercise to try to see where the blockages in the supply chain are," said Maila.
A healthworker at St Elizabeth Gateway Clinic in the Eastern Cape told patients she had been told that the district's stock of efavirenz had been left at the Mthatha depot "because there was no space in the delivery truck".
Meanwhile, the shortage of lamivudine in Mabopane and Winterveld, has been blamed on an influx of patients to these clinics after the closure of the Hope for Life Clinic, which was previously supported by the US President's Emergency Plan For AIDS Relief (Pepfar).
However, lamuvidine shortages were also experienced in Daveyton, Etwatwa and Soweto as well as in Secunda and Barberton in Mpumalanga. Some Mpumalanga clinics also reported shortages of the ARV tenofovir.
Olga Monyane, a patient at Dube clinic in Winterveld, said she was worried she was going to die because she had been turned back a number of times when visiting the clinic to collect medicine.
The Democratic Nursing Organisation of South Africa (Denosa) expressed concern at the ARV shortage in Gauteng, saying nurses were being labeled as "uncaring professionals that deprive patients of medication", when the problem lay with suppliers.
"In the East Rand, some patients have gone for a week without taking ARVs due to shortage of supply of medication. A number of nurses have to either turn back patients or convey the bad news to them that there is not enough medication, which often triggers anger among communities," said Denosa in a statement.
"Most concerning to DENOSA about the shortage of medications in some clinics is the possibility that some patients may develop resistance to crucial and life-saving medication such as ARVs."
Denosa called on the Public Protector to look into the stockout "as part of her investigation into health, as there won't be any positive outcomes for patient treatment in an environment that doesn't have enough supply of medication".
Meanwhile, the Democratic Alliance says the ARV shortages, if allowed to continue unchecked, "could impact on the lives of tens of thousands of South Africans".
"Continued delivery delays and shortages could increase the amount of people dying of AIDS related diseases, as well as the amount of drug-resistant HIV cases in South Africa," said the DA's Patricia Kopane.