The race to become governor of Indonesia's capital was neck and neck in early counting on Wednesday and heading for a second round between the incumbent Christian governor and a Muslim former education minister, sample counts showed.

The Jakarta poll has been overshadowed by religious tensions, with mass Islamist-led protests against Governor Basuki Tjahaja Purnama, an ethnic Chinese Christian.

The vote is also being widely seen as a proxy battle for the 2019 presidential election.

Purnama had secured 42.57 percent of the votes, just ahead of former minister Anies Baswedan in second place with 40.23 percent, based on a quick sample count of around 40 percent of the vote by private polling firm SMRC.

The other candidate, Agus Yudhoyono, was in third place with 17 percent. Other pollsters showed similar results.

A candidate needs to get more than 50 percent of the votes in the first round to win outright.

The job of governor can be a springboard to the presidency and weeks of campaigning have been overshadowed by mudslinging, political intrigue and rising hardline Islamist sentiment, raising questions about the role of religion in politics.

"We hope that everybody can return as a family after these elections," President Joko Widodo said after voting in Jakarta earlier on Wednesday.

Purnama was a deputy to Widodo when he was the previous Jakarta governor and Widodo's party is backing him.

Purnama has been campaigning while on trial on a charge of insulting the Koran, a case that has brought Muslims onto the streets, urging voters to shun a non-Muslim as leader.

He denies the charge and after dipping in opinion polls his support rebounded, which analysts attribute to his record of improving the bureaucracy and easing congestion and flooding in Jakarta.

Indonesia has the world's largest Muslim population but is officially secular and home to minority Christian and Hindu communities, as well as hundreds of ethnic groups.

Baswedan is backed by a former general who Widodo beat in the last presidential election in 2014, Prabowo Subianto, who is promising a comeback to the national stage.

The elections in the capital, alongside scores of other regional polls in the world's third-largest democracy, were peaceful and mostly running without hitches, police said.

Police had deployed 75,000 personnel across Indonesia with 16,000 in Jakarta, concerned hardline Muslim groups may again take to the streets to oppose Purnama.