The Gauteng provincial government has conceded that there is a crisis within its health department, but premier Nomvula Mokonyane has defended her decision to retain health MEC Ntombi Mekgwe.

The rot did not lie with the political leadership, but that individuals in the department had to account, Mokonyane told reporters in Pretoria on Tuesday.

"This is a department which employs more than 15,000 professionals. It is very easy for people to say when there is a challenge, fire the MEC and the real culprits get away with murder," she said.

In her state of the province address on Monday, Mokonyane announced that the health department was being split from the social development department, and that Mekgwe would remain health MEC.

She said a major shake-up was imminent across key departments, including social development, roads and transport and health.

In what she described as "a mismatch" in departmental skills allocations, Mokonyane said some people did not have the requisite competency for their positions.

"You find that this person with a senior position in transport... cannot even draw a road. That is why services are outsourced and we have to pay the huge bills," she said.

The premier said massive irregularities had also been unearthed in public health institutions like the Chris Hani Baragwanath Hospital, where doctors were bringing in their own patients from private medical institutions and treating them with state resources.

Mokonyane said many nurses at the government hospitals came to work "just to sit around and save their energy" for the time they went on duty at private institutions.

She said R25-million was saved in December when the authorities discovered how the overtime claims system was being abused by hospital staff.

"We have now introduced new systems on how people check-in for work. People would claim overtime and get paid for time they had not spent at work," she said.