A deputy presiding officer at a voting station in Benoni, Johannesburg, has been removed following an investigation into the transfer of special votes.

This after a video showing a party agent assisting with the transfer of the special votes went viral on Monday.

The video shows a party agent helping to transfer special votes, in their double envelopes from a ballot bag used during home visits, to a ballot box in the voting station.

The Electoral Commission of South Africa (IEC) said, while the transfer of the special votes from bags to ballot boxes was a normal procedure, handling of the electoral material by any party agent was prohibited.

"They [party agents] are only allowed to observe operations and raise objections. The Deputy Presiding Officer who was overseeing the process has therefore been removed," the IEC said in a statement on Tuesday.

The IEC said that, despite the breach, it was confident that the integrity of the election had not been undermined, as special votes had a very strict verification process prior to the counting of ballots through the double envelope system.

It explained that all special votes were first placed in an unmarked envelope, which was then inserted into a second envelope, which was marked with the voting station and voter’s particulars for verification.

The envelope was then placed in the ballot box or bag, if it was a home visit.

Before special votes are included in the count they are subjected to thorough verification against lists of authorised special voters. 

"This is witnessed by party agents and observers. Only when the special vote is confirmed against the authorised list, is the outer envelope removed and the inner envelope is added to normal ballots for counting," it added. 

The IEC said it was also investigating instances where the double envelope system had not been used in some special votes on Monday, as well as some ballot papers which may not have been stamped at the back.