Jakarta's Christian governor today looked set to lose office to a Muslim former government minister in a highly divisive election that has been going on while the Christian is on trial for blasphemy.

So-called 'quick counts' by 10 research companies show former Cabinet minister Anies Baswedan winning between 55 and 60 per cent of votes with about 80 per cent of ballots counted, according to AP.

The incumbent, Basuki 'Ahok' Tjahaja Purnama is currently on trial after allegedly insulting the Quran and hundreds of thousands protested against him in Jakarta, deriding his Chinese ancestry and calling for him to be imprisoned or killed.

Ahok congratulated his opponent and told a televised news conference: 'We now will come together and forget this campaign. Jakarta is home for all of us.'

Baswedan, who is from a moderate Muslim background, capitalised on the backlash against Ahok by courting the support of conservative clerics and figures on the radical fringe who opposed electing a non-Muslim, AP noted.

Ahok, who was Jakarta's first ethnic Chinese governor and first Christian in half a century, has been popular with middle-class Jakartans for his efforts to stamp out corruption and make the highly polluted capital, home to 10 million people, more agreeable to live in.

On Thursday, prosecutors will make their sentencing demand in Ahok's trial. Blasphemy is a criminal offence in Indonesia and punishable by up to five years in prison.

In a speech to fishermen in September, the governor reportedly cited a verse from the Quran that warns Muslims against taking Christians and Jews as allies. He is said to have added that due to Indonesia's transition to democracy in 1999, it was perfectly acceptable for Muslim voters to choose a Christian in the election for governor in February.

Ahok has denied the charges, saying that his comments were aimed at politicians 'incorrectly' using the Quranic verse against him.

Blasphemy convictions in Indonesia almost always result in conviction, and the law has been criticised by Amnesty International for hurting freedom of expression and for targeting religious minorities.

Indonesia technically guarantees freedom of religion in its constitution but in reality only six religions are recognised and tough blasphemy laws control debate and target minorities.

Christians represent less than 10 per cent of the 250 million population.