The University of Cape Town (UCT) announced that vice-chancellor Professor Mamokgethi Phakeng was admitted to hospital and given time off from her duties.
Phakeng is receiving medical attention and was given time to recuperate from stress.
UCT's council was informed at a special meeting on Tuesday night.
Council chairperson Babalwa Ngonyama said: "Given the stress, the vice-chancellor has been under, this time away from the office will also serve to give her a bit of rest."
Tuesday's council meeting appointed deputy vice-chancellor Professor Elelwani Ramugondo as acting VC.
"Along with the UCT senior leadership team, I have no doubt that the university is in capable hands during the vice-chancellor's absence. The university council is united in stabilising the situation and is concerned for Professor Phakeng's health," she said.
Phakeng is under increasing pressure after the UCT council voted to appoint a retired judge and independent panel to probe allegations of misconduct against her and Ngonyama.
At the heart of the probe was whether Phakeng and Ngonyama misled the university's executive and Senate about the reasons for the departure of the deputy vice-chancellor for teaching and learning, Associate Professor Lis Lange. They said Lange resigned for personal reasons, while Lange claims she was pushed.
The university is yet to make a formal announcement about the independent probe.
UCT spokesperson Elijah Moholola told News24 the university council is continuing to work on the process of setting up an independent panel as per the resolution taken in October.
"This process is ongoing. Council will give an update on this process as and when there are further developments," he said.
News24 understands retired Supreme Court of Appeal president Lex Mpati is expected to chair the probe alongside two retired judges, Sisi Khampepe and Azhar Cachalia.
Governance expert Trish Hanekom and Wits head of transformation Bernadette Johnson have also been asked to join the panel.
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