"President Jacob Zuma is not sick and these are routine annual checkups he has been scheduled to undertake for a man of his age," Mac Maharaj, presidential spokesperson, told the Mail & Guardian.
The name of the hospital was not disclosed.
Zuma (70) recently apologised during his State of the Nation address last month about having flu.
Although he has the constant use of senior South African National Defence Force medical personnel at his disposal, Maharaj said they were not equipped to deal with the tests the president was undergoing.
"They don't carry x-ray machines and that type of thing with them wherever they go, so the president has been admitted to a hospital to be attended to by a team of specialists," he added.
"The president was given a clean bill of health by his doctors," said Maharaj.
Hospital in Durban
Members of the media started inquiring about Zuma's health after a report on SAfm that he was in a hospital in Durban.
Zuma was expected in Cape Town later on Wednesday.
"He has concluded his [medical] visits and will now travel to Cape Town, where he is to open the National House of Traditional Leaders, among other duties," said Maharaj.
Maharaj also said there is no cause for concern and the president will be back at work as soon as these tests are concluded.