Voters swamped polling stations in post-apartheid South Africa's most exciting elections on Wednesday, but fears emerged by mid-afternoon that ballot papers and boxes were running out.

Election officials also lamented a "few criminal challenges" marring the "carnival mood" across the country.

"We have a few criminal challenges that face us. That has never happened to us. It is the first time," Independent Electoral Commission chairperson Brigalia Bam told reporters in Pretoria.

At some places, ballot boxes disappeared in apparent election fraud, while in other areas, ballot boxes were too full to cope with a high turnout.

An electoral officer was arrested and charged with fraud at Ulundi in KwaZulu-Natal, a traditional Inkatha Freedom Party (IFP) stronghold where pre-1994 clashes with African National Congress (ANC) supporters ended in tens of thousands of deaths.

In Nkandla, the hometown of ANC leader Jacob Zuma, an area manager lost all her voting material. In the same area, some 50 marked ballot papers were found, said Bam.

Chief electoral officer Pansy Tlakula said the incidents were a "drop in the ocean" of the 58-million ballots that had been printed.

"A carnival mood is prevailing across the country," said Tlakula, adding that more than 98% of the 19 726 voting stations countrywide opened on time at 7am.

23-million South Africans have registered to vote.

But by late afternoon, reports emerged that voting stations at both Gauteng, the Free State and Mpumalanga were running out of ballot papers.

Bam said there were "very, very long queues" in Gauteng.

"So long that in some areas they ran short of ballot papers... papers have been sent [to replenish]," said Bam.

Gauteng chief electoral officer Sy Mamabolo said voter turnout had been so high that ballot boxes were too full.

Election officials were in talks with political parties about a safe process to empty the boxes, he added.

Provincial electoral commissioner Terry Tselane said voting hours in Gauteng would not be extended beyond the poll closing time of 21:00, but if voters were still in queues by 21:00, they would not be turned away.

"It is my opinion that by 21:00 every registered voter would have voted," he said.

However, if voters were still in queues at voting stations after 21:00, the presiding officers would allow them to vote, he added.

In the Free State, the Democratic Alliance (DA) said some voting stations had already run out of ballot papers.

"Growing numbers of the bigger voting stations have already run out," said DA CEO Ryan Coetzee.

He said this was according to what the province's electoral officer Chris Mepha had told a provincial party liaison committee.

Comment from the provincial IEC was not immediately available.

Mpumalanga's provincial electoral officer Steve Ngwenya earlier warned: "We may run short of ballot papers too - we are doing an estimate. We did expect a large turnout today [Wednesday] but there were more special votes than we thought yesterday [Tuesday], so boxes were used for them," said Ngwenya.

The Western Cape's electoral officer, Courtney Sampson, said that a last-minute concession allowing people to vote at the polling station of their choice was causing major headaches.

"It really is posing problems," Sampson said.

He was speaking after the provincial ANC called on the commission to "minimise" long queues on the Cape Flats.

"The ANC is concerned that these long queues may result in some people turning away and not casting their votes," the ANC said in a statement.

Election officials earlier in the week predicted a very high turnout in the fourth general elections since the advent of democracy in 1994.

Voters seemed to heed President Kgalema Motlanthe's call to turn out in their droves.

"You can't improve any situation by keeping away... It's like missing the off-ramp and five years is a very long time," said Motlanthe, who voted in Pretoria, where long queues were reported across the city.

But the stars of the elections were Jacob Zuma and South Africa's first democratically elected President, Nelson Mandela, who both received Hollywood-style welcomes at voting stations.

Zuma said: "When I grew up, I did not know that this day would come.

"This makes me feel great and it's a feeling far different from the one that we had under the apartheid government."

Journalists struggled to hear Zuma, amid pushing and shoving, above the screaming of his supporters who were trying to touch him.

Mandela cast his vote without a word, walking into a scene resembling a Hollywood paparazzi scramble as hundreds of photographers and journalists competed with voters waving cellphone cameras for a picture.

Described as the most exciting elections since the advent of democracy in 1994, Wednesday will test the strength of the ANC and the impact of a new breakaway party, the Congress of the People, on the political landscape.

It was co-founded by sympathisers of axed President Thabo Mbeki, who made a rare public appearance since his dismissal last September to cast his vote.

Mbeki was in a jovial mood when he cast his vote in Parktown, Johannesburg, laughing when a brave reporter asked him who he had voted for.

"I am sure that [question] is unconstitutional, this is a secret ballot," said Mbeki, as he was crowded by cameras.

"I think the future of our country depends in part on people voting according to their conscience," Mbeki added.