Sipho Ngwema, spokesman for the FBI-style Scorpions unit, said Mark Thatcher, 51, was arrested early on Wednesday after police arrived to search his home in an upscale Cape Town suburb.
"We are looking for information ... we are looking for computer files, telephone records and so on that are going to assist us in our investigation," Ngwema told CNN television.
Thatcher, a controversial businessman who moved to Cape Town from the United States in 1996, "reacted like anyone else would react when confronted with police", Ngwema said, adding he was expected to appear in court later on Wednesday.
Thatcher, whose mother was UK prime minister from 1979-90 became Sir Mark when he inherited his baronetcy upon the death of his father Denis last year.
Police are investigating Thatcher on charges of violating South Africa's tough anti-mercenary law in connection with what officials have called a plot to overthrow President Teodoro Obiang Nguema Mbasogo of Equatorial Guinea, sub-Saharan Africa's third largest oil producer.
Mark is the son of former British
premier Margaret Thatcher
Eighty four foreigners, mostly South Africans, have been put on trial simultaneously in Zimbabwe and Equatorial Guinea in one of Africa's most spectacular mercenary cases for decades.
"We have alleged that he (Thatcher) is a financier in that particular coup attempt ... we are looking for documents that are going to assist us in our investigation. We take this very seriously," Ngwema said as his colleagues searched the house.
"He should not use our country as a springboard to export violence and disorder," he added.
Privately educated at Britain's elite Harrow School but with little academic success, Thatcher failed his accountancy examinations three times.
"He should not use our country as a springboard to export violence and disorder"
spokesman, Scorpions Unit
Thatcher, who the British media dubbed "The Boy Mark," is adored by his mother. He tried a number of jobs including car rally driver.
When her son got lost in the Sahara desert during a sports car rally in 1982, the "Iron Lady" broke down and wept in public.
Just how he financed his Rolls Royce lifestyle has been a matter of rumour and innuendo for years in Britain which he left in the mid-1980s for the United States to escape media attention.
British media reports have suggested he earned millions in lucrative arms deals.