Voters in Madagascar headed to the polls on Thursday in a presidential election boycotted by 10 out of 12 opposition candidates and marred by weeks of violent protests.

People queued at polling stations in areas supporting President Andry Rajoelina and his Tanora MalaGasy Vonona (Young Malagasy People Ready) party, while those in opposition neighbourhoods were mostly empty. There was a low-key security presence across the capital.

Rajoelina, who is seeking a third term, warned opponents that trying to prevent people from voting was unlawful as he cast his vote flanked by his wife and children.

"A handful of people tried to prevent citizens from expressing their choice. They have the right not to participate but the populations have the right and the duty to vote," he said after voting in Antananarivo's northern neighbourhood of Atmobe.

Rajoelina faces growing isolation after leading opposition figures, including two former presidents, declared him unfit to run and called on their supporters to abstain from voting.

Rija Ralijaona, a 26-year-old day labourer, said she expected whoever wins the election to reduce unemployment.

"I expect the next president to create jobs for young people," she said, as she prepared to cast her vote at dawn.

Calls by the opposition to postpone the elections were echoed by the organisation grouping Madagascar's four biggest Christian churches, which declared on Wednesday that it would not observe the vote, citing an unsuitable political environment and lack of standards.

Rajoelina, a 49-year-old entrepreneur and former DJ, rose to power in a 2009 coup that scared off investors in the Indian Ocean island. He stepped down after almost five years as leader of a transitional authority and then became president after winning a 2018 election.

His opponents say he should be disqualified because he acquired French nationality in 2014.

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.

Over the past six weeks, police have used tear gas to break up regular protests by opposition supporters.

The United Nations human rights office last month said Malagasy security forces had used "unnecessary and disproportionate force" against peaceful protesters and called for respect for freedom of expression and assembly. The government said its duty was to maintain order.

Provisional results are expected to be released on November 24, said Soava Andriamarotafika, a spokesperson for the Independent National Electoral Commission.