With 93.25 percent of the votes counted, Electoral Commission chairwoman and Supreme Court judge Anastansia Msosa declared the winner at 1 a.m. Friday (2300 GMT Thursday).
Malawians went to the polls Tuesday to chose between re-electing Mutharika or replacing him with a candidate backed by his predecessor — the latest round in a five-year feud that has triggered rioting, an impeachment effort and parliamentary paralysis.
Mutharika won 2,730,630 of the votes counted, or 66 percent, compared to the 31 percent, or 1,270,057 votes, cast in favor of veteran opposition leader John Tembo.
Earlier Thursday, Tembo alleged voting had been rigged. Election officials said they were investigating his claims.
Mutharika is to be sworn in at 10 a.m. Friday (0800 GMT), government officials said.
Soon after the announcement of the 75-year-old Mutharika's re-election, more than 100 supporters clad in the blue color of his Democratic Progressive Party erupted into a spontaneous cheer and broke into song and dance in the streets.
Tembo, 77, was a leading figure in the dictatorship of Hastings Kamuzu Banda, who ruled from the end of British rule in 1964 until 1994.
He also has the backing of Mutharika's predecessor and rival, Bakili Muluzi — who in 2004 had supported Mutharika's first run for the presidency.
Earlier Thursday, Muluzi's United Democratic Front issued a statement congratulating Mutharika. Muluzi entered into an alliance with Tembo's Malawi Congress Party after he was barred from contesting these elections after having already served two consecutive five-year presidential terms.
But at a later news conference, Tembo said he would not accept the results as he believed there had been vote rigging.
Tembo said he had information that, in some constituencies, Mutharika and his parliamentary candidates won more votes than the number of registered voters.
"These elections have been rigged, we can't accept to be cheated," he said.
At the announcement of the results, election commissioner Msosa acknowledged "some challenges" during the electoral process such as irregularities in the voting roll. However, she commended Malawians for holding a peaceful election.
International observers agreed the poll had been peaceful and said it was well-managed. However, they raised concerns about the use of state resources to favor Mutharika's party in the campaign.
"We are extremely concerned at the conduct of state-owned media in its coverage of these elections," said former Ghanaian president John Kufuor, who is chairman of the Commonwealth Observer Group, from countries that were former British colonies.
The two fell out after Mutharika won the 2005 vote, with Muluzi's help, and arrested senior officials of Muluzi's party on fraud and corruption charges. Muluzi himself is being tried on charges of siphoning $10 million from donor countries but insists the charges are politically motivated.
There were five other presidential candidates, including
Nearly six million voters were registered; they were also choosing members of the 193-seat parliament.
According to the latest results in the ongoing count, Mutharika's DPP had won 78 seats against the 18 for Tembo's MCP. Muluzi's UDF got only 12 seats with the northern-based
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