The civilian, a motorcycle ride-sharing driver, was hit at the site of violent clashes on Thursday near parliament as police sought to disperse demonstrators protesting about issues including lawmakers' pay and education funding. 

The protests on Friday afternoon prompted a number of schools in the capital to allow students to leave early and banks and businesses to ask employees to work from home. The military has been deployed in some areas, visuals broadcast by local media showed.

Drivers, students in colourful jackets and people from other walks of life descended on the country's House of Representatives building and police headquarters in Jakarta to stage protests on Friday, throwing rocks at the gates and chanting "Killer! Killer!"

Wearing their signature green jackets, drivers also staged protests in other cities, including Bandung and Surabaya on Java island and Gorontalo on Sulawesi.

After darkness fell, heavy rain in Jakarta dispersed some students and drivers from the police headquarters, though a few remained keeping alight a fire built from tyres and bamboo while singing patriotic songs.

Police fired tear gas at protesters trying to enter the headquarters.

Protesters torched a house belonging to the People's Consultative Assembly legislative wing in Bandung, state news agency Antara reported. Local media also reported a police post was set on fire in Makassar city, on Sulawesi. 

Motorcycle driver Pendi Nasir, 43, who was among the protesters in Jakarta, called for a transparent investigation from the police over the death of the driver, Affan Kurniawan.

"We don't want our colleagues here to become victims of this riot again," he told Reuters, calling for action against those at fault. 

Stand-up comedian Aci Resti attended a protest at the parliament against a generous housing allowance for lawmakers.

"I'm here to voice the opinions of my friends, who are fed up with everything, with the members of the House of Representatives, with everything, with the government," she said.

Protesters were undeterred by earlier remarks by Prabowo calling for calm, expressing condolences for Affan Kurniawan's death and ordering a thorough probe of the incident.

"I am shocked and disappointed by the excessive actions of the officers," Prabowo, whose presidency nears its one-year anniversary in October, said in a video message. "I have ordered a thorough and transparent investigation ... and officers involved must be held accountable."

The unrest has rattled investor confidence in Indonesia's economy. The rupiah closed 0.9 percent weaker against the dollar at 16,495, while the stock index fell as much as 2.3 percent to hit its lowest point since August 12, before finishing down 1.5 percent. 

"If Prabowo isn't careful ... protests may devolve into chaos," Made Supriatma, a visiting fellow at the ISEAS-Yusof Ishak Institute in Singapore, told Reuters.

President Prabowo visited the family of ride-hailing motorcycle driver Affan late Friday to pay his condolences. He earlier urged calm, promising an investigation into his death.

Earlier on Friday, thousands of drivers gathered near the police mobile brigade headquarters in Central Jakarta on Friday, demanding accountability for Affan's death, as officers cordoned off a stretch of road nearby.

Police fired teargas in an attempt to disperse protesters, mostly motorcycle taxi drivers known locally as "ojeks".

"I joined the protest because I'm very concerned about the death of my fellow driver," 52-year-old Muzakir told AFP. 

"We demand justice for Affan, for the perpetrators who ran him over to be tried as fairly as possible, and to be fired from their institution."