Votes are being counted in Burkina Faso after Sunday’s presidential and legislative elections, where threats of extremist violence prevented parts of the country from casting ballots.

Election workers began the counting after polls closed by holding the ballots up for observers and marking the votes on a chalkboard beside the candidate’s name. Preliminary results are expected within the next two days.

While there were no reported incidents of major attacks, threats of violence linked to al-Qaeda and the so-called Islamic State prevented people from casting ballots in the North, Sahel and East regions.

Newton Ahmed Barry, president for the National Independent Electoral Commission, said that nearly 3,000 polling stations which were expected to open yesterday did not.  This prevented up to 350,000 people from voting.

In Tapoa province in the east, 224 polling stations out of 335 didn’t open, according to a report from Codel, a local organisation monitoring the elections.

Codel said it was “concerned about the situation in areas weakened by insecurity”.

Local officials in the Sahel and Centre North – the epicentres of the violence – told the Associated Press that people were angry about not being able to vote.

Saidou Wily, a government official in Barsalogho town in the Centre-North, said: “I’m upset and people are complaining because they thought they’d be able to vote and couldn’t.”

At least 37 villages in the region expecting to vote were unable to, he said.

Other polling stations which opened had to close early due to security concerns. In Markoye Commune in the Sahel’s Oudalan province, the polls closed three hours ahead of schedule, according to a post-election report from human rights organisation West African Network of Peace building.

There were also reports of fights between political activists in the West and Centre North, and attempts to “influence voting” by supporters of candidates and political parties, according to an internal report from a local human rights group.

Halidou Ouedraogo, president of Codel, said there were some areas in the east where no ballot paper was available so approximately 30 people voted on fake ballots. But this was detected and rectified, he said.

Observers say that this election is a major test for the nation’s young democracy in the face of rising extremist attacks. The violence and intimidation show how limited the authorities’ control and legitimacy really are, experts warn.

Alex Thurston, assistant professor of political science at the University of Cincinnati, said: “(Whoever) wins… will confront the challenge not just of restoring security but also showing Burkinabe that every citizen matters.”

President Roch Marc Christian Kabore has promised to secure the country and is vying for another five years against 12 other candidates.

Mr Kabore is expected to win but the opposition hopes to split the vote, depriving him of the 51% support needed for an outright victory in the first round. It then plans to form a coalition behind the strongest opposition candidate for the second round.

A change in Burkina Faso’s electoral code this year means that election results will be valid even if people can’t vote in parts of the country.

However, Zephirin Diabre, a leading candidate from the opposing Progress and Change Party, accused the ruling party of fraud and bribery. He also accused the National Independent Electoral Commission of making changes to the electoral map.

After voting in Ouagadougou, Mr Diabre told the media that he will congratulate whoever the winner is but “won’t accept results that are stained with fraud and irregularities”.