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The favourite of Madagascar strongman Andry Rajoelina was leading run-off presidential polls with two-thirds of ballots counted on Thursday, though both candidates claim victory and accuse the other of fraud.
Hery Rajaonarimampianina, 55, had 51.69 percent of votes according to results in the afternoon, after Friday's vote to restore democracy following Rajoelina's coup in 2009.
His rival Robinson Jean Louis, 61, candidate of ousted president Marc Ravalomanana, won most votes in the first round on October 25 but trails by three percent in the run-off.
Only half the island's 7.9 million eligible voters cast their ballot.
Final results are only expected in January, but both candidates have already declared themselves the victor, with both sides claiming votes were rigged against them.
International observers gave the December 20 vote the greenlight, and called on the parties to respect the electoral process.
The Indian Ocean island has been an international pariah since Rajoelina seized power from Ravalomanana in an army-backed coup four years ago.
The two were blocked from running in this year's polls for fear of a return to violence. Instead, each has supported a candidate who ran under their colours.