Protests by residents of Bronkhorstspruit, east of Pretoria, are not over water shortages, the water affairs department said on Wednesday.

"These are protests about the billing system and the Tshwane municipality has taken up the matter from that perspective," spokesman Mava Scott said.

"Several news reports are wrongfully reporting that the people are protesting about water shortages... ."

Several buildings had been set alight during protests in the area. Two people were arrested in Rethabiseng on Wednesday and would be charged with public violence and illegal public gathering. Police stopped residents marching to the main road in the area to voice their dissatisfaction on Wednesday.

The City of Tshwane said on Tuesday residents of Bronkhorstspruit, Rethabiseng and Zithobeni in Region Seven had been protesting because they were unable to buy pre-paid electricity.