The National Sea Rescue Institute (NSRI) said a volunteer rescue crew was dispatched at 11:30 am after reports of a shark incident in Jeffreys Bay in the Eastern Cape region.
"On arrival on-scene remains of a body, believed to be those of an adult male, have been recovered from the water and handed into the care of the police and the forensic pathology services," it said.
According to eyewitnesses, the man had been snorkeling at the time of the attack.
Last year there were four shark attacks in South Africa, three of them fatal, according to the International Shark Attack File at the Florida Museum of Natural History.