La Nyalla Mattalitti fled the country in April after he was named as a suspect in a corruption case that dates back to 2012 when he was the chairman of the chamber of commerce in East Java province, said Amir Yanto, a spokesman for the attorney general's Office.
Mattalitti is accused of embezzling 387,000 dollars from the chamber.
He has denied the charges. He was deported from Singapore on Tuesday for overstaying his visa and questioned at the attorney general's office, Amir said.
The Indonesian Football Association (PSSI) has been embroiled in a legal tussle with the Sports Ministry, who suspended the organisation last year over its refusal to ban two clubs from a league competition.
The suspension prompted world football governing body FIFA to ban Indonesia from international competitions. The suspension and the FIFA ban were lifted last month after the PSSI successfully appealed.
- DPA