Outgoing deputy Local Government Minister Godfrey Kamanya shot himself in his home, according to police.
His spokesman denied reports that his suicide was linked to him apparently losing his parliamentary seat.
Official results have not yet been declared in what was expected to be a tight presidential race.
The BBC’s Raphael Tenthani in Malawi says the electronic counting system has broken down in some areas and votes are being collated manually in these places.
Mr Kamanya left a suicide note at his home in the capital, Lilongwe, asking President Joyce Banda to take care of his daughter and provide for her education, our reporter says.
Eleven candidates ran against Mrs Banda, but her main challenger is Peter Mutharika, the brother of former President Bingu wa Mutharika.
The Malawi Election Commission (MEC) will announce results when 30% of votes have been counted, its chairman Maxon Mbendera said on Wednesday.
The MEC was “not anywhere in the neighbourhood” of that figure, he added.
Counting was being done manually because the electronic system was “refusing to take the information from the ground where our data clerks are stationed to send the results,” chief elections officer Willie Kalonga told the AFP news agency.