Early counting from a small number of polling stations put Rajaonarimampianina in a distant third place behind leading contenders Andry Rajoelina and Marc Ravalomanana, both also former presidents of the Indian Ocean island.
![Vladimir Putin has dominated Russian politics for a quarter of a century [Getty Images]](data:image/svg+xml;charset=utf8,%3Csvg%20xmlns%3D'http%3A%2F%2Fwww.w3.org%2F2000%2Fsvg'%20width%3D'100'%20height%3D'100'%20data-ring-placeholder%3D'1'%3E%3C%2Fsvg%3E "Vladimir Putin has dominated Russian politics for a quarter of a century [Getty Images]")
"Many voting irregularities and technical anomalies have been detected including an invalid electoral register... intimidation (and) the presence of pre-ticked ballots," said Rajaonarimampianina, who ruled from 2014 to September 2018.
"All indications are that the votes of the Madagascan people have been stolen," he added in a statement issued the day after the poll.
"We will not let the people be robbed of their vote," he warned.
With only 291 of the 24,852 polling stations counted by Thursday afternoon, Rajaonarimampianina had obtained 3.29 percent of the votes counted so far.
Rajoelina had 45.07 percent and Marc Ravalomanana was on 40.3 percent, according to official figures.
Thirty-six candidates ran in the election, which is considered an acid test of the democratic credentials of the impoverished island that has a history of coups and instability.
Independent monitors have yet to give their verdict on the fairness of the vote.
Bitter rivals
A candidate must reach 50 percent to win outright, otherwise a second round will be held on December 19.
Ravalomanana, 68, and Rajoelina, 44, are bitter rivals. It is the first time they have faced each other at the polls.
Ravalomanana ruled from 2002 to 2009 until he was ousted in a military-backed coup that installed Rajoelina who was in power until 2014.
Rajaonarimampianina succeeded him, ruling until earlier this year.
Both Ravalomanana and Rajoelina were banned from contesting the last elections in 2013 under international pressure to avoid a repeat of political violence that engulfed the island in 2009.
Campaigning for Wednesday's polls passed off without incident and voting was peaceful.
Before polling day, around 20 lower-profile candidates had called for the vote to be delayed over alleged problems with the electoral roll.
Attempts by Rajaonarimampianina to change the island's electoral laws backfired this year, sparking nearly three months of sometimes violent protests in the capital Antananarivo.
The demonstrators forced Rajaonarimampianina to accept a "consensus" government tasked with organising the election.
Madagascar is one of the world's poorest countries, according to World Bank data, with almost four in five people living in grinding poverty.
The former French colony has struggled to overcome political divisions after a disputed 2001 election that sparked clashes and the 2009 coup.
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![33 passengers and one crew member died on the dive boat, Conception [Brian van der Brug/Los Angeles Times/AP]](data:image/svg+xml;charset=utf8,%3Csvg%20xmlns%3D'http%3A%2F%2Fwww.w3.org%2F2000%2Fsvg'%20width%3D'300'%20height%3D'172'%20data-ring-placeholder%3D'1'%3E%3C%2Fsvg%3E "33 passengers and one crew member died on the dive boat, Conception [Brian van der Brug/Los Angeles Times/AP]")
