Representatives of the European Union and regional bloc SADC welcomed Friday's vote, despite organisational hiccups preventing some from casting their ballots to end a four-year political and economic deadlock.
"The elections were free, transparent and credible," said the EU's head election observer Maria Muniz de Urquiza.
"Despite certain difficulties in the organisation, the vote went well," she said, presenting a preliminary report.
The EU hailed a "calm" campaign period and election day, she said, despite isolated incidents of violence.
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"A non-negligible percentage of Malagasies are not listed on the voters' roll," she said.
"The whole of the voter potential has not been registered," she said of the 7.8 million voters out of the vast Indian Ocean island's 22 million people.
Meanwhile the Southern African Development Community (SADC) "concludes that the Madagascar elections were peaceful, calm, fair and transparent, and reflect the will of the people," according to Netumbo Nandi-Ndaitwah, the head of its observer mission.
The SADC brokered a transitional government after strongman Andry Rajoelina seized power in an army-backed coup in 2009.
By today afternoon ousted president Marc Ravalomanana's candidate Robinson Jean Louis was leading with 27 percent, after under eight percent of the 20,000 voting stations reported results.
Hery Rajaonarimampianina, of Rajoelina's party, was second with just under 16 percent, suggesting an eventual run-off poll.