Saiful Mahdi, a lecturer from Aceh province, was imprisoned for three months over comments made in a WhatsApp messenger group chat among fellow academics, which criticised a hiring process for lecturers.
Saiful's case prompted complaints over the ease at which people can be prosecuted in Indonesia for comments made on messaging platforms, including remarks about people not even identified.
Amnesty International has called the law was "deeply flawed."
Indonesia's chief security minister Mahfud MD on Tuesday (Oct 5) said Jokowi, as the president is known, had approved amnesty for Saiful and would await feedback from parliament before granting a pardon.
Asked why Jokowi favoured amnesty in Saiful's case, a presidential spokesman referred Reuters to the security minister.
A presidential amnesty was given in 2019 to a woman jailed under the same law for recording lewd phone calls from her boss.
The 2008 electronic information and transactions law was designed to regulate online activity, including defamation and hate speech.
Between 2016 and 2020, there were 786 cases involving the law, with 88 per cent of the those charged ending up behind bars, according to Damar Juniarto of digital advocacy group, the Southeast Asia Freedom of Expression Network.
Jokowi has said he wants to revise the law this year.
The government has formed a task force to oversee that and provide guidelines for law enforcers to apply the law more judiciously.
Syahrul, Saiful's lawyer, told Reuters his client appreciated the amnesty, without which his experiences could "adversely impact academic and speech freedom."
He said 38 scholars in Australia wrote to the president, requesting Saiful's pardon.
Saiful's wife, Dian Rubianty, was in tears during an online seminar and said his case "has stolen sleep away from me and my children."