Malawi's opposition alliance claimed victory for its candidate Lazarus Chakwera on Thursday in a re-run of the 2019 presidential election, annulled by courts because of fraud.

The vote on Tuesday came to be regarded as a test of the ability of African courts to fight ballot fraud since Malawi's judiciary infuriated President Peter Mutharika in February by overturning the result of last year's vote.

"With all votes ... tallied, it is now clear that Malawians have resoundingly given (the opposition)...alliance the mandate to govern this country for the next five years," a statement from Chakwera's Tonse Alliance said.

"Malawians have at last reclaimed their destiny."

A spokesman for Mutharika's alliance did not immediately respond to a request for comment. Malawi's state and private media on Wednesday gave Chakwera a comfortable 55% lead, with nearly three-quarters of votes counted, against Mutharika's 40%.

At a news conference on Thursday, Electoral Commission chairperson Chifundo Kachale urged Malawians to wait for the official result, which was taking time to collate because the ballots had to be transported back to head office from locations across the lakeside southern African nation.

A win for Chakwera would be a dramatic reversal of last year's discredited poll that handed the presidency back to the incumbent, who has been in power since 2014.

Electoral officials said voting day on Tuesday was largely peaceful, apart from some sporadic reports of violence in opposition strongholds, and Malawi has remained calm while awaiting the result.

The cancelled result forced a change in the electoral system, swapping a "first-past-the-post" for a system in which the winner has to get more than 50% of the vote.