John Tembo (l) will not accept a victory for President Mutharika (r)
Malawi's main opposition party has called for the release of results from Tuesday's general election to be stopped, citing "irregularities".
The Malawi Congress Party says its election agents were denied access to counting centres in its traditional stronghold in the Central Region.
Several MCP parliamentary candidates have lost their seats in the area.
The MCP presidential candidate said he would not accept President Bingu wa Mutharika being declared the victor.
The presidential contest between the two men had been seen as the closest in the country's history.
John Tembo is backed by ex-President Bakili Muluzi, whose attempt to run for a third term was blocked by the courts.
While it is still among the poorest nations, Malawi has one of the fastest-growing economies in the world and Western donors hope its relative stability over the past decade will not be disrupted.
Chief Election Officer David Bandawe said the electoral commission would investigate the MCP complaints.
Results have been released from just 1% of the 3,897 polling stations around the country.
President Mutharika has 34,585 votes against 10,954 for Mr Tembo.
Earlier, John Kufuor, team leader for the Commonwealth observer group, told the BBC he had been concerned with the media coverage during the election process.
"The major handicap, we thought, was lack of coverage of the parties outside the government," he said.
AFP news agency reported that police had raided a radio station owned by Mr Muluzi shortly before polls opened.
The agency cited police as saying three members of staff had been arrested at Joy Radio, and was told by an editor that a tape of a satirical programme had been seized.
The election follows a long political feud between Mr Mutharika and his predecessor Mr Muluzi that has caused riots, a failed impeachment bid, parliamentary deadlock and coup plot claims.
Mr Muluzi lost a court battle on Saturday to be able to stand for a third term, having argued in vain that after a break of five years, he should be able to run for office again.
His United Democratic Front has endorsed Mr Tembo, leader of the Malawi Congress Party, which governed the country for 30 years.
Mr Mutharika fell out with his one-time backer in 2004, accusing Mr Muluzi of trying to stonewall an anti-corruption drive.
Mr Muluzi is being tried on charges of siphoning $10m (£6.5m) from donor countries, but insists the charges are politically motivated.
Mr Mutharika quit his rival's party in 2005 to form his own Democratic Progressive Party and lead a minority government.
The 75-year-old former World Bank official, who has won praise from Western donors, says he only wants one more term and will then retire.
Mr Tembo, 77, once a leading figure in the regime of the late dictator Hastings Kamuzu Banda, is hoping the election will bring to an end 15 years in opposition.
Poverty, agriculture and health care are the big issues for Malawi, where two-thirds of the population lives on less than a dollar a day and Aids has orphaned an estimated one million children.
In the parliamentary election, about 1,100 candidates, including a record number of women, are standing but no party is expected to win an outright majority.
There are five other candidates in the presidential race but two have already conceded that President Mutharika has won.
Final results are expected by Thursday.