"It's most likely to affect small businesses, such as spaza shops, disproportionately," said Beverage Association of SA executive director Mapule Ncanywa.
The proposal is out for comment until 22 August.
A study by the Priceless unit run by Wits University's professor Karen Hofman showed that a tax of 20% on sugared drinks could result in a decrease of more than 220,000 in the number of obese adults.
But Ncanywa contended that the effect on weight would be negligible because only 3% of the average South Africans' energy intake was from sugared drinks.
Hofman said the industry's job loss estimates "are implausible and hypothetical".
The industry said that a sugar tax in Denmark was scrapped in 2014 because it did not reduce sugar intake. Instead, Danes crossed the borders to buy sugared drinks.
Defenders and opponents of the sugar tax cited studies of a similar tax in Mexico to make their point.
Industry studies of the effects of a sugar tax have not been published independently or peer-reviewed.