Malawi’s president is demanding a vote recount after alleging a national election this week was marred by rigging, though the election commission has dismissed the allegation.

Joyce Banda said on Thursday that irregularities included a failure to inspect voter registers at some polling centres, efforts to prevent election monitoring and the hacking of the electronic counting system in the impoverished African country.

The country’s election commission says the vote was fair and that it will have a “clear picture” of the outcome in the next few days.

The Malawi president has called for a recount just days after a general election amid allegations of vote-rigging and computer hacking.

“It has come to my attention that there (are) some serious irregularities in the counting and announcement of results in some parts of the country … In light of these concerns – and concerns emerging from other stakeholders, which includes other political parties – I call upon the Malawi electoral commission to carry out an immediate manual audit of the whole process,” Joyce Banda said.

Her comments follow reports that her main rival, Peter Mutharika, was showing an early lead in preliminary unofficial results from the poll on 20 May.

According to the data, Banda is on the brink of losing a hard-fought election that pitted her against three other political heavyweights.

Banda, a philanthropist and former vice-president, came to power in April 2012 after the sudden death of the former president, Bingu wa Mutharika. She was hailed by donors as an example of good leadership before the country became embroiled in a multimillion-dollar corruption scandal known as Cashgate.

Twelve candidates are vying to become president, with Banda among the four frontrunners. Peter Mutharika, a popular contender and the brother of the former president, was allowed to enter the leadership race despite facing trial for treason.

If Banda is defeated, she will become the first serving female African head of state to have lost an election. Equality campaigners have raised concerns that her departure from office could set back women’s empowerment. “It will send a wrong message about women running for office. Joyce Banda had created a platform for women to climb the ladder of leadership,” said Benedicto Kondowe, an education and human rights activist.

The voting chaos piles further pressure on the Malawi electoral commission (MEC). The military was deployed on Tuesday after voters burned some polling stations amid allegations of rigging when some bureaus opened up to 10 hours late.

Election officials had announced previously that the electronic vote-tallying system had broken, forcing them to resort to fax and email, and delaying the release of results. The system “is refusing to take the information from the ground where our data clerks are stationed to send the results”, the chief elections officer, Willie Kalonga, said after the vote.

Banda claimed the information system that the MEC intended to use for the management of the results of the poll had been jammed deliberately, “thereby limiting the monitors’ ability to effectively carry out their duties”. “We have seen gross and unwarranted allegations of rigging, misinformation and negative propaganda all aimed at undermining the credibility of the electoral process,” she said.

Voting irregularities included non-availability and non-inspection of the voter register at some polling centres, Banda said, resulting into some people voting two or three times, and “serious anomalies where some candidates were winning by voters whose numbers exceeded the total number of the registered voters at the centres”.

Banda called on Malawians to remain calm until the commission determined the outcome of the poll. But in some areas, such as the volatile Ndirande township in the capital, Blantyre, voters protested against the chaotic poll by setting fire to tents, furniture and buildings.

“I am quite happy now that I have voted for a leader of my choice. I didn’t vote for Banda as she has no idea of how to run a country … and giving her five years would have been a waste,” said Daile Phiri, a street vendor selling Chinese electric items in the township.

The high court judge who chairs the MEC has dismissed Banda’s call for a recount. Maxon Mbendera said the president’s allegations were untrue and claimed her People’s party was acting out of desperation.

He said the system had not been hacked, but was rendered useless after it developed technical glitches that was slowing the processing of the results. “We have switched to manual and we will start announcing the results after we have received 30% of the results,” he said. EU monitors said the electoral process had “considerable organisational shortcomings and a few isolated incidents of unrest”.

Véronique De Keyser, chief observer of the EU election observation mission, said lack of essential materials resulted in delays in the opening of polling stations amid a challenging environment.

The country, with 28 districts, had 4,445 polling centres where about 7 million people cast their votes.

Separately, reports surfaced on Thursday that Godfrey Kamanya, the former local government deputy minister, had killed himself as unofficial partial results showed he was losing his parliamentary seat in Lilongwe.

Police sources said he shot himself at about 3am after it was clear he had lost the poll as a candidate for the People’s party.

Tuesday’s poll was the fifth to be held in the south-east African country since the Kamuzu Banda dictatorship ended 20 years ago.

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