Former health minister Robinson Jean Louis, candidate of ousted president Marc Ravalomanana, told AFP he expected to win 56 percent, while his opponent Hery Rajaonarimampianina claimed to have taken between 60 and 65 percent.
"There has been massive fraud," Jean Louis told AFP, adding that "an entire airplane" filled with ballots pre-marked in favour of his rival had been discovered.
His campaign held an early victory party yesterday night.
Meanwhile, the camp of Rajaonarimampianina, a former finance minister under strongman Andry Rajoelina, denied any wrongdoing.
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The election commission, security forces, and international observers have not confirmed incidents of fraud after hailing generally peaceful polls though with little turnout.
"There are a lot of rumours, but these were elections to exit a crisis and there will always be rumours," the UN representative for Madagascar, Fatma Samoura, said.
Observer missions will release their main conclusions tomorrow.
Madagascans voted yesterday in parliamentary and run-off presidential polls to return the island to democracy after Rajoelina seized power in an army-backed coup from Ravalomanana in 2009.
The run-off coincided with a vote for 151 parliamentarians after an inconclusive first round on October 25.
Initial results today gave Jean Louis the lead with 50.21 percent of votes but only 204 polling stations out of 20,001 reporting.
The election commission should announce final results by January 7, to be confirmed by the election court by February 18.