Simukai Nyasha, a spokesman for Zimbabwe's National Parks Authority, said: "The deceased and his hunting party unknowingly got in the middle of a breeding herd of elephants with several calves".
Botha was a highly regarded houndsman, and frequently led leopard and lion hunting safaris with his pack of dogs for his company Game Hounds Safaris.
In response, another member of Botha's hunting group fired a fatal shot, Afrikaans news site Netwerk24 reported. He was working as a hunting agent for Kuronda Safaris owned by Zimbabwean hunter Mr Tim Shultz.
Theunis Botha, 51, was a well known hunter from Johannesberg in South Africa.
A fourth cow was said to have lifted Botha with her trunk.More news: White House Announces US Embassy Will Not Move to Jerusalem - For Now
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A crocodile was later shot in the area and DNA results of the animal's stomach contents matched the missing hunter, the BBC reported. Scott van Zyl was leading a crocodile hunt in the Chikwaraka camp when he disappeared, the report noted.
A year ago a tourist, Stephen Coetzee was trampled to death by a female elephant in Hwange National Park.
Botha is survived by his wife Carika and their five children, all who live in Tzaneen, South Africa.
Mr Coetzee, from Bulawayo who was in company of his brother, Christian and a female friend was killed as he tried to take pictures of the jumbos.
Villagers in Hwange and the surrounding nearby areas often complained of losing livestock and crops to elephants in the area.