Mutharika had 40.49 percent of the 75.81 vote count, while opposition leader Lazarus Chakwera had 35.44 percent, according to the ongoing count by the Malawi Electoral Commission.
Coming a distant third is President Mutharika’s own vice, Saulos Chilima, who has so far bagged over 651, 124 votes. He was contesting under a newly registered UTM Party.
Mutharika, who leads the ruling Democratic Progressive Party (DPP), campaigned for a second five-year term on his record of improving Malawi's scant road and power infrastructure.
Chakwera on Wednesday warned of alleged attempts to rig the election, saying his Malawi Congress Party (MCP) was conducting its own count that showed he was ahead.
Malawi has a "winner-takes-all" system and in 2014 Mutharika won with 36 percent of the vote.