Six people are dead and at least 200 injured in civil unrest in the Indonesian capital after the election commission confirmed President Joko Widodo had won last month’s election, according to Jakarta’s Governor.

Indonesia’s Election Commission on Tuesday said Mr Widodo had won a second term with 55.5 per cent of the vote in the April 17 election.

It was announced about 2am, which was believed to be in an effort to avoid mass rioting.

Mr Widodo warned protesters he would not tolerate anyone disrupting security, the democratic process and the unity of Indonesia following rioting in Jakarta.

“We will not give any space for rioters who try to damage our country, the state of unity of the Republic of Indonesia,” he told reporters on Wednesday night.

“There is no choice, the military and police will take firm action in accordance with the law.”

Earlier, crowds swelled in central Jakarta with some protesters carrying wooden poles, while others had smeared toothpaste around their eyes, apparently to protect themselves from tear gas.

The majority of the protesters appeared to have come from outside Jakarta and police found envelopes containing money on some of the people they searched, National Police spokesman Muhamad Iqbal told a news conference.

“This is not a spontaneous incident, this is something by design. There are indications that the mobs are paid and bent on causing chaos,” he said.

Mr Widodo won more than 85 million votes of 154 million cast in the world’s third-largest democracy, but retired general Prabowo has alleged “massive cheating and irregularities”. 

Mr Prabowo’s legal director has said his campaign plans to contest the result in the Constitutional Court.

On Monday, an election supervisory agency dismissed claims of systematic cheating, citing a lack of evidence. Independent observers have said the poll was free and fair.

Islamist groups, many of which support Mr Prabowo, have in the past been able to mobilise hundreds of thousands of supporters.

Presidential Chief of Staff Moeldoko said he believed there was “a systematic effort by a certain group … that is riding on the situation to muddy the situation”, adding that authorities had seized two pistols from people involved in riots.

Protests that began calmly in the sprawling textile market neighbourhood of Tanah Abang on Tuesday turned violent after nightfall, with police firing tear gas to disperse the crowd.

Fadli Zon, deputy chairman of Gerindra, Mr Prabowo’s political party, accused police of initiating an attack on protesters and said he found 171 bullets, including live rounds, when he visited the area on Wednesday morning.

“The public have a right to demonstrate. They are people who are concerned by cheating. They are not mobilised, paid or facilitated,” Mr Zon said.

Prabowo campaign spokesman Dahnil Azar Simanjuntak called on “all sides to hold back and not commit violence”.

Police spokesman Dedi Prasetyo said that security forces on the ground, including military personnel, were not armed with live bullets.

Indonesian authorities say 40,000 police and army personnel are on duty across Jakarta to maintain security.

Chief security minister Wiranto said the government had temporarily blocked certain social media functions to prevent inflammatory hoaxes and fake news

–with AAP