Voting in Burundi’s presidential election passed calmly on Wednesday despite simmering political violence, the coronavirus pandemic and the opposition accusing the authorities of fraud.

In what could be the first competitive presidential election in Burundi since a civil war erupted in 1993, the ruling CNDD-FDD party's candidate, retired general Evariste Ndayishimiye, is running against opposition leader Agathon Rwasa and five others.

President Pierre Nkurunziza, whose government has repeatedly been accused of rights abuses, will step down after 15 years.

Rwasa said electoral observers from his party were chased away from the polling stations.

"There is a massive electoral fraud. Our representatives, mandated to follow the electoral process to the end, have been chased. So how can you agree on results counted out of your sights?" he told Reuters.

The government did not respond to requests for comment about the fraud accusation.

Last week it expelled the head of the mission in Burundi of the World Health Organization, who had criticized all parties for holding rallies despite the coronavirus pandemic.

Burundi has reported 42 coronavirus cases and one death. But only 633 tests have been carried out, according to the Africa Centres for Disease Control and Prevention. The authorities said it was safe to vote despite the disease and called on Burundians to turn out.

"We call on Burundians to vote in massive numbers and vote peacefully. We need good elections," Pierre Claver Kazihise, chairperson of the election commission, said in comments aired by state broadcaster RTNB.

Queues to vote were long in the morning in the main commercial city Bujumbura's Musaga neighbourhood, where the opposition is popular.

"The voting is really taking place smoothly and I voted for change but I am pessimistic about the counting of votes," said one resident who did not wish to be identified.

Several voters were worried that Twitter and WhatsApp - messaging services that can spread information quickly - seemed to be shut down.

The election is meant to usher in the first democratic transition in 58 years of independence, after widespread international criticism of the last election in 2015, when Nkurunziza won a third term and the opposition boycotted.

That election sparked violent protests that drove hundreds of thousands of Burundians into exile. The United Nations documented hundreds of killings and the torture and gang-rape of opposition activists. Donors withdrew funding.

The government denies accusations of rights violations.

Burundi’s population is divided between majority Hutu and minority Tutsi ethnic groups, as is its neighbour Rwanda. Both major candidates in Wednesday's vote are former leaders of mainly Hutu rebel militia groups.

The United Nations and the African Union said on Sunday they remained "concerned about reports of intimidation and violent clashes between supporters of opposing sides".

There were few international election monitors after the government said they would have to spend 14 days in quarantine to prevent the spread of the coronavirus.

Full results are expected within a week. If no one wins 50% in the first round then a run-off is held within a fortnight.