Malians have voted in a runoff presidential election to determine if incumbent Ibrahim Boubacar Keita will remain in office in the sprawling West African nation threatened by rising extremist violence.

Mr Keita faced off against opposition leader Soumaila Cisse.

Sunday’s polls had low turnout by closing amid attacks and threats of violence by Islamic extremists.

The chairman of Arkodia village in the north Niafunke commune in Timbuktu region was killed, four election workers were physically harassed and the polling station there was burned, according to the Citizen Observation Pool of Mali, which had more than 2,000 observers.

The organisation reported several incidents on Sunday.

Two polling stations were burned in Keltamba and election officials were harmed by gunmen in Ngouma commune in central Mali, observers said.

Ibrahim Boubacar Keita casts his ballot
Ibrahim Boubacar Keita casts his ballot (Annie Risemberg/AP)

In north and central Mali, more than 50 polling stations had closed before noon because of the threats by extremists in those regions, the organisation said.

In the polling centres covered by its observers, the organisation said the participation rate was about 8.1%.

It said 14.4% participated in Timbuktu, and only 4.8% in Bamako.

However, their observers did not cover all voting areas, and the election commission has not yet given its estimate of voter turnout.

In the July 29 first-round presidential vote, extremists killed three election workers and destroyed some voting materials.

Nearly 43% of voters made it to the polls last month and at least 671 polling stations were closed.

Despite the relatively low turnout, officials called the vote well-conducted.

Mali has grown more insecure since Mr Keita beat Mr Cisse in a second-round election in 2013.

Malian authorities arrested three jihadists on Friday who said they were preparing to carry out an attack during the vote in Bamako, said Mali army spokesman Colonel Idrissa Traore.

Soumaila Cisse casting his vote
Soumaila Cisse casting his vote (Boubacar Sada Sissoko/Union for the Republic and Democracy via AP)

Extremists are staging more bold attacks that have spread to central Mali, where both Islamic State and al Qaida-linked militants are present.

Deadly communal clashes between ethnic groups and accusations of heavy-handed counter-terror operations have caused even deeper tensions and mistrust of the state.

Still, a second term for Mr Keita, 73, seems likely.

He received 41.7% of the vote in the first round from a field of 24 candidates and has gained endorsements from some other candidates.

Dressed in his traditional white boubou, Mr Keita voted near his home in Bamako on Sunday.

“I hope that everyone will be very vigilant,” he said, saying that any suspected attempts at fraud should be reported to police.

“Ultimately this election must end as it should, with the celebration of democracy … This is what we hope for in our hearts.”

Mr Cisse, 68, who placed second in the first round with nearly 18% of the vote, has blamed Mr Keita for insecurity, violence and corruption.

His opposition party also alleges there was voting fraud in July.

Mr Cisse has not received major endorsements from failed candidates but does have the backing of a popular spiritual leader, Mohamed Ould Bouye Haidara.

“This time, I have a good feeling,” Mr Cisse has said.

A man casts his ballot in Mali
A man casts his ballot (Annie Risemberg/AP)

His campaign director Tiebile Drame claimed there were cases of stuffing of ballot boxes in several northern locations.

However, the constitutional court on Wednesday said it has registered more than 10 requests from the opposition over various anomalies in the first round, but most were declared inadmissible.

On Saturday, the opposition organised a march “to warn against the fraud”.

Issa Namory Keita, a 57-year-old retiree, said he would vote for the incumbent Mr Keita.

“Unlike his challenger, my candidate knows the country well and it is he who has the solution to the problems,” he said.

Another voter who was unrelated but with the same family name, Fanta Keita, said she will also vote for the current president.

“He is a man who loves his country, he is a worker who has opened several development sites and I hope he continues his work,” she said.

Voter turnout trickled throughout the day and was expected to remain low.

Some people have fled areas of violence until the vote is over.

In central Mali, attacks have become more frequent amid communal clashes as neighbours suspect one another of being recruited by extremist groups.

Meanwhile, Malian soldiers in recent months have been accused of abuses, including extrajudicial killings, during counter-terror operations.

On Wednesday, armed men attacked the Boni prefecture, according to a Malian security official, killing the prefect’s secretary.

Malian authorities have tried to reassure the public and encourage them to go to the polls for the second round.

Residents in central Mali, however, have said they do not see the increased security.

Many in the municipalities of Pignariba, Lowel-Gueou and Bara-Sara said they probably would not be able to vote.