Hery Rajaonarimampianina had won more than 53 per cent of the vote after ballots from more than 96 per cent of polling stations had been tallied.
According to figures on the electoral commission's website, which are still to be validated, his rival Robinson Jean Louis, 61, who is backed by ousted leader Marc Ravalomanana, was trailing by 6.6 per cent.
The polls are meant to pull the Indian Ocean island out of a political and economic crisis brought on by Rajoelina's army-backed power seizure in 2009.
"We find that the atmosphere is generally positive but there are also cases where the candidates are not happy with the results that are being published," said regionally appointed mediator Leonardo Simao.
But the Southern African Development Community (SADC) mediator called on candidates to allow the proper electoral bodies to rule on allegations of fraud.
Jean Louis failed in a bid to freeze the release of partial results while ballots were inspected.
Today he prepared to present evidence directly to the public in a special two-hour live broadcast on two private television channels.
"We want to prove that the election happened to be quiet, but not transparent, there was massive fraud."
Despite the mud-slinging, international observers gave the vote the green light and called on the parties to respect the electoral process.
The island's two main political players -- Rajoelina and Ravalomanana -- had been barred from running in the polls amid fears of a return to violence.
They instead backed proxy candidates who went head-to-head on December 20 after an inconclusive first round in October.
Only half of the island's 7.9 million eligible voters cast their ballot.
Rajaonarimampianina, 55, is an astute businessman and former finance minister under Rajoelina, while Jean Louis is a doctor and former health minister under Ravalomanana.