The 49-year-old entrepreneur and former DJ rose to power on the Indian Ocean island in a 2009 coup, stepped down after almost five years as leader of a transitional authority, then won a 2018 election.
The opposition says he should not have run again in Thursday's poll because he acquired French nationality in 2014 — which they say automatically revokes his Malagasy one — and has created unfair election conditions.
He says both accusations are baseless political tactics.
In preliminary results from the electoral commission CENI, Rajoelina had garnered more than 72.9% of the estimated total of 6.2% counted so far.
Votes counted so far indicated a turnout of 39.5%, compared to 55% in the equivalent first round of voting in 2018.
'Enthusiasm not there'
There were 11 million people out of a population of roughly 30 million registered to vote in this year's polls, which were preceded by weeks of opposition-led protests.
This photograph taken on November 16, 2023 shows ballot papers laid down during the counting process at a polling station in Antananarivo, during the first round of the Madagascar presidential election.
Of 12 opposition candidates originally, only two took part in the vote. One was Marc Ravalomanana, the former president ousted in 2009, the other Siteny Randrianasoloniaiko.
"Enthusiasm was not there," said Andriamanambe Raoto, editor-in-chief of Politika, a monthly publication.
The United States voiced concern on Thursday over low turnout, inadequate training for election staff and irregularities by party officials.
The opposition said participation was the lowest in Madagascar's history and vowed to keep protesting.
Rajoelina says the constitution does not require the head of state to exclusively hold Malagasy nationality, and that any loss of nationality is subject to signed authorization by the government.
The opposition also called for changes to the makeup of electoral commission and for the formation of a special court to hear election disputes.
Regional observer groups did not respond to requests for comment on the early results. Full provisional results are expected on November 24 while the High Constitutional Court is due to certify them on November 30.