The general election has run very smoothly on Wednesday apart from a few minor glitches, the Independent Electoral Commission said.

"Things are still so far in progress with only very minor isolated and manageable incidences that are being reported," IEC chair Brigalia Bam said.

As yet it was still too early to judge voter turnout, said Bam, but judging by reports from electoral officers there appeared to have been a good turnout, she said.

By late afternoon there were still reports of long queues in North West, the Northern and Eastern Cape, Limpopo and Gauteng.

She said even traditional hotspots like Nongoma in KwaZulu-Natal were very quiet.

Bam said the IEC had even sent deputy chairman Herbert Vilakazi to the region to monitor it and he reported that things "were very normal".

Complaints however had been received from various provinces concerning the theft of ballot papers, bar code tampering and biased electoral officials.

Chief Electoral Officer Pansy Tlakula said police were currently investigating a case in which five ballot books, each containing 100 papers, had gone missing in the Northern Cape.

"The IEC wishes to point out that each ballot paper must be validated with an IEC stamp. Without such a stamp they cannot be counted," she said, adding that they also needed to be reconciled at the end of the voting process. Bam said a number of electoral officials had also been removed from their posts.

"In KwaZulu-Natal three presiding officers resigned of their own accord, five declined to sign a code of conduct binding them not to actively canvas or work for a political party and four were dismissed for performance related matters," she said.

Another presiding officer and his deputy were dismissed in the North West province when 22 ballot papers were stolen on Tuesday near Vryburg.

These were later returned by a voter.

Election parties have remained at each others throats complaining of election irregularities.

The Inkatha Freedom Party and Democratic Alliance have accused the African National Congress of electoral fraud where they allegedly attempted to lure voters away in KwaZulu-Natal with promises of free cold drinks.

The ANC fired back when it raised concerns that the allegations "may be intended to lay the basis for a rejection of the election results should they not favour the IFP."

In the Free State four DA members were arrested and released after four hours in jail when they allegedly drove into a voting station with a car advertising the DA.

They accused the ANC of instigating their arrest and lengthy detention - Sapa.