Deputy Agriculture Minister Pieter Mulder is not fit for office, the African Farmers' Association of SA (Afasa) said on Tuesday.
"He must immediately do the honourable thing and resign," Afasa president Mike Mlengana said in a statement
"This will give him time to revisit [the] history of this country wholly and not selectively."
Mulder, also the leader of the Freedom Front Plus, said in Parliament last week that "Bantu-speaking" people had no historical claim to 40 percent of South Africa's land.
Mlengana said: "As African farmers, we are extremely saddened and astonished by the deputy minister's remarks."
The issue of was a thorny and highly sensitive one, he said.
The National Emergent Red Meat Producers Organisation (Nerpo) supported Afasa's call for Mulder to resign and described his conduct as "regrettable", especially coming from a Cabinet minister.
"His regrettable conduct leaves us with a serious doubt that he is ready to serve in government," said Nerpo managing director Aggrey Mahanjana.
On Monday, ANC general secretary Gwede Mantashe also took a swipe at Mulder for his remarks.
Launching a book on the ANC's centenary, Mantashe said the first war of resistance was fought in 1659 by the Khoi and the San people.
"He [Mulder] believes the genocide that followed that war left no Khoi and San people... He believes there were no people left."