The Indonesian President has accused "political actors" of taking advantage of a large-scale Jakarta demonstration, after it turned violent last night.

Estimates of up to 150,000 people marched through the capital on Friday, shutting down major streets as they demanded the immediate jailing of Jakarta's governor over comments he made about the Koran.

While tensions had flared throughout the day with pockets of protesters occasionally hurling sticks and water bottles at police, it was largely peaceful throughout the day.

But violence began breaking out after night fell when the remaining demonstrators refused to disperse.

Police vehicles were set alight, rocks, sticks and bottles began to be thrown and tear gas and a water canon was fired on the rioters.

Thousands of protesters from various Islamic organizations rallied in front of the Indonesian Presidential Palace. (AAP)

One elderly man reportedly died from the effects of tear gas while several others, including a number of police, were injured.

President Joko Widodo- said he was thankful for the rally being peaceful during the day.

But, he said, he "regretted the unruly situation later in the evening because the public who were supposed to disperse themselves turned violent."

"Political actors are taking advantage of the situation," the Jakarta Post reported him as saying after midnight..

The demonstration was supposed to finish at 6pm but in the early hours of Saturday some were still occupying parts of the city.

Basuki Tjahaja Purnama, commonly referred to as Ahok, is the capital's straight-talking Christian governor who is ethnically Chinese Indonesian.

Tensions over his leadership were inflamed when he said in late September that his detractors were using a verse in the Koran to manipulate followers into not voting for him.

The verse has been interpreted by some to mean Muslims should not elect a non-Muslim leader.

Ahok has apologised and insisted he meant no offence, but he is currently under investigation for blasphemy charges.

Riding into the crowd on top of a truck with large loudspeakers attached to it, the head of the hardline group the Islamic Defenders Front (FPI) Rizieq Syihab said: "We want the president to order the police to jail Ahok right away. Don't make the excuse of not being able to interfere".

The protests are spurred on by the militant Islamic Defenders Front and came about because Muslim hardliners want Jakarta governor Basuki Tjahaja Purnama, known as Ahok, to be punished for allegedly insulting the Koran. (AAP)