Indonesian President Prabowo Subianto has expressed regret over the death of a civilian during protests in the capital Jakarta and ordered an investigation against a police officer who fatally struck a motorcycle taxi driver with an armoured vehicle.

Prabowo said on Friday that the officers involved must be held accountable, as he was shocked and disappointed by the excessive actions of the officer.

A 21-year-old motorcycle taxi driver, Affan Kurniawan, was killed after being hit by a police armoured vehicle on Thursday.

Indonesian police chief General Listyo Sigit Prabowo also issued an apology to the victim's family and the public and said the incident will be thoroughly investigated.

Thousands of Indonesian workers rallied on Thursday outside the parliament in Jakarta to protest low wages, outsourcing practices, and rising perks for lawmakers, which ended after the death of the taxi driver.

However, on Friday morning, a crowd again gathered in front of the police headquarters and staged a protest against the killing of Affan.