Novel Baswedan was attacked by two assailants on a motorcycle after leaving a neighbourhood mosque, Jakarta police spokesman Argo Yuwono said. He said police are still investigating.
Baswedan's face was heavily bandaged when he was photographed at a hospital. Local media described the incident as an acid attack.
The Corruption Eradication Commission is currently prosecuting a case in which it alleges about 80 conspirators and several companies stole more than a third of the funds provided for a USD 440 million electronic identity card system in 2011 and 2012.
The names were revealed in an indictment presented to a special corruption court last month at the start of a trial of two Interior Ministry officials.
Jokowi condemned the attack on Baswedan as "barbaric" and said he has ordered police to capture the assailants.
A statement from the commission said it "strongly condemns the barbaric act". They described it as a form of terror and part of efforts to weaken the commission.
Baswedan was arrested by the national police in May 2015 when he was accused of fatally shooting a detainee while serving as a police officer in Bengkulu province in 2004.
A public uproar resulted in police dropping the case. Many activists believed police were seeking revenge for Baswedan's role in investigating corruption among senior officers.
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