The culling of an estimated 20 000 pigs in the Eastern Cape started in Idutywa on Monday, after an outbreak of swine fever hit the province.
At least 3 500 emerging farmers' pigs have been affected by the virus, and strict control measures to stop the spread of the disease have been set in place.
"We have started the process of culling about 12 000 pigs in the Eastern Cape rural town of Idutywa," said Eastern Cape senior veterinarian Lubabalo Mrwebi.
The virus has spread to an area bounded by the Kei River in the south, Mbashe River in the north, the N2 in the west and the eastern seaboard, it was reported on South African Broadcasting Corporation radio news on Monday.
Mrwebi said sodium hydroxide was being used to spray vehicles and the shoes of people moving through Butterworth, Willowvale, Idutywa and Qolora.
The were checkpoints at Butterworth (Ibika and Bethel College), Willowvale, Idutywa (Fort Malan and the Willowvale Road) and at Kei Mouth's Ferry point.
Mrwebi said the outbreak in Transkei had started in the Centane district, near Qolora.
Officials were expected to move to Queenstown on Tuesday, the report said.
Prominent Eastern Cape pig farmer David Osborne, speaking to the South African Press Association on Monday night from his Queenstown farm, said he was "not
happy about the reports".
"At this stage, a lot of the things that are being said are not correct."
Osborne said he did not "want to pass comment" and would call a press conference when "I've got my ducks in a row".
"People can't go around saying things that are not true. Things are different from what one has been led to believe."
Osborne was reacting to radio reports that the swine fever virus, which last occurred in South Africa in 1918 before an outbreak in the Western Cape a month ago, had affected his pigs.
Speaking on the SABC's Vuyo Mbuli show on Monday, Mrwebi said the virus could have spread from Cape Town harbour.
Mrwebi said a truck containing pig swill left Cape Town "every Monday" for the Eastern Cape and returned on a Thursday.
Asked if there were "chinks in the armoury of the [swill] monitoring process," Mrwebi replied that the source of the virus was "open to speculation".
He stressed, however, that the virus could not have come out of East London or Port Elizabeth harbours.
"It is likely to have come from the Western Cape."
Osborne, with pig farms in Aliwal North, Cookhouse and Queenstown, also farms beef on "five or six farms" in the Queenstown district, according to his beef manager Colin Steven.
The disease affects only pigs and has no effects on humans or other animals.