Malians are preparing to vote in a runoff election that will go ahead on Sunday despite widespread allegations of fraud in the first round.

The current president, Ibrahim Boubacar Keita, won 41% of the vote in the first round on 29 July, with Soumaila Cissé a distant second with 18%. The pool of candidates has now been reduced from 24 to two, and it is the first time an incumbent president of Mali has ever had to face a runoff.

Around 250,000 people, 3% of the electorate, were unable to vote because of insecurity in central and northern Mali, and Cissé has accused Keita of stuffing ballot boxes there.

“The ballot box-stuffing explains IBK’s tallies in the north and centre,” a spokesman for Cissé told AFP when the complaint was filed, using the president’s initials as many do in Mali.

Malian soldiers stand guard at a polling station in Bamako, Mali, on 29 July 2018. Photograph: Mohamed Messara/EPA

18 of the 24 candidates demanded the resignation of the electoral chief, calling the vote an “electoral hold-up”, but the constitutional court ruled on Wednesday that the runoff should go ahead, saying that most of the complaints had been received after the 48-hour deadline.

Aliou Diallo, a mining tycoon who came third in the first round, told Malians to “vote as they wish” while Cheick Modibo Diarra, who came fourth, said that replacing Keita with Cissé was “just a game of musical chairs”, dashing some Malians’ hopes of an opposition coalition to unseat the president.

Mali is still reeling from its annus horribilis, 2012, when it went through a Tuareg rebellion, a civil war and a military coup, and lost control of the north.

Cissé is from Timbuktu, the ancient city of learning that was controlled by jihadists for ten months, in which time they banned music, imposed sharia law and destroyed important cultural monuments.

Although whoever wins will technically be president of the entire vast west African country, in practice the government has never regained control of the north, though some security is provided by the French counter-terrorism force Operation Barkhane, and a UN peacekeeping mission that costs $1 billion per year.

In the lead-up to the election, the UN warned of a surge in intercommunal violence in the central region of Mopti, with hundreds of people killed, shot or burned alive in their homes. In June, Mopti was also the target of a suicide bomb that killed five people near the entrance of the local headquarters of the G5 Sahel, a regional fighting force that has struggled to get up and running partly because of cash flow problems.

Malian Opposition leader Soumaila Cisse waves to supporters during a presidential campaign meeting in July 2018 in Mopti. Photograph: Issouf Sanogo/AFP/Getty Images

EU observers demanded that the government release the results of the first round polling station by polling station, but when they finally released the results, it did not provide the number of registered voters at each station, making it impossible to verify the true turnout.

According to the government, however, only 43% of Malians cast their vote.

Partly this was because of insecurity, but analysts say it can also be explained by voters’ disillusionment with corruption and the increasing gap between them and elites in the capital.

Bamako, in Mali’s south-west, is isolated from the north and centre, and leaders in neighbouring Niger complain that they are more affected by the spillover of violence than Malian politicians, who tend to stay south.