The department's director-general, Precious Matsoso, told the parliamentary standing committee on appropriations that the healthcare system had 45,733 vacant posts, and 351,925 filled posts - an 11.5% shortfall.
Limpopo has the highest number of vacant posts, 10,074, with 35,458 filled; and
Eastern Cape has 7,005 vacant posts and 39,293 filled;
Gauteng has 6,100 vacant posts and 68,000 filled.
It is not known if the posts are vacant because of a lack of funds or a lack of skilled people.
The posts include those for doctors, nurses, optometrists, audiologists, administrators, physiotherapists, financial and hospital managers, and maintenance workers.
DA MP Alan McLoughlin said: "It is known that as people resign from their jobs in hospitals and clinics, they are not replaced."
The SA Medical Association has been saying for at least a year that vacant posts were not being filled.
Association spokesman Mark Sonderup said: "We have been raising this issue of frozen posts since 2016.
"You will recall it has been denied repeatedly by the minister. He even called me personally at one stage asking where I had obtained such false information. I guess it wasn't fake news after all."
At a press conference in February last year Health Minster Aaron Motsoaledi denied that vacant posts were not being filled.
He said: "We want to put it on record that there are no medical posts frozen in this country ... If there is freezing of posts by government departments, they have nothing to do with medical doctors as posts in the health sector are exempted."
But director-general Matsoso told parliament:
The risk of medical negligence lawsuits increased with the shortage of staff;
Two state-of-the-art buildings in the Free State could not be opened because there were no health workers to staff them; and
The department's budget was declining as increases were not keeping up with inflation.
Matsoso said health spending had risen faster than economic growth and providing healthcare would become unaffordable without systematic reform.
"If the current trends continue, the health sector will have to reduce its services," she said.
National Freedom Party MP Shaik Emam said it was clear that budget allocations for health were far less than required.
"But provinces are not financially well-managed and money is being wasted," he said.
A specialist working in a state hospital said having staff shortages was "exhausting, completely and utterly exhausting".
"Patient numbers keep increasing but budget cuts limit what we can do for them."
According to the minutes of the meeting of the parliamentary committee, Matsoso said there were too few health technologists in some provinces to perform important work on health equipment.
An official from the office of the auditor-general told MPs there were staff shortages in clinical engineering units in all provinces except Gauteng and the Western Cape, so maintenance of medical equipment was not undertaken.
The official urged that vacancies in financial departments be filled to prevent irregular expenditure.
South Africans suffer both from infectious diseases common in developing countries, such as TB, and non-communicable diseases typical of wealthy countries, such as diabetes, high blood pressure and heart attacks. This "colliding epidemics" was straining the health system, said Matsoso.
One new doctor said: "My internship was done at a very understaffed hospital. It certainly affects morale. It makes you hate getting up in the morning and makes you feel hopeless - no matter how hard you work, it will never be enough. You can't do the work of three people."