Incumbent President Peter Mutharika is set to win a second term in the impoverished, landlocked southeast African state. With most votes counted, he led his main challenger by five percentage points.
With 75% of votes counted, 78-year-old Malawian President Peter Mutharika had a 40% share. That put him ahead of his main rival, former Christian pastor Lazarus Chakwera with 35%, according to the electoral commission on Thursday.
Saulos Chilima, who was Mutharika's closest ally before the men fell out last year, had taken 18%. The president can not fire his deputy, so the 46-year-old stayed on as vice president as he set up his own youth-focused United Transformation Movement to fight the election.
Malawi has a "winner takes all" system. Mutharika won his first term in 2014 with just 36% of the vote.
The 64-year-old Chakwera said attempts had been made to manipulate the results and that his Malawi Congress Party, had conducted a separate count which showed him to be ahead.
No data has been published so far to show how many of the registered 6.8 million Malawians turned out to voteon Tuesday to elect a president for a five-year term, a new parliament and local government councillors.
Malawi, together with neighboring Mozambique and Zimbabwe are still recovering from the effects of Cyclone Idai which hit the southeast coastal areas of Africa in March.
Mutharika stood on a platform of improving the road and power infrastructure: "My priorities for this country are development and building skills," he said at his final rally before the vote. However, he has also faced accusations of nepotism and corruption.
Malawi won independence from Britain in 1964 and was ruled by Hastings Banda as a one-party state until elections in 1994. With a population of 18 million and one of Africa's poorest economies, Malawi has a million adults living with HIV, one of the highest rates in the world.