Football Association of Indonesia (PSSI) President La Nyalla Matalitti has been accused of corruption by judicial authorities as the national body continues to be torn apart by a wave of scandals.
The PSSI was suspended by world football body FIFA last May following a row with the Sports Ministry of Indonesia.
The Government tried to replace the existing governing body, plagued with allegations of corruption and mismanagement.
This was a necessary step for the future of the sport in the country, they claimed.
FIFA, who are strongly against political interference within its Member Associations, banned the PSSI after the Government refused to lift their suspension of the PSSI.
Matallitti was arrested following allegations he misused grants from the Indonesian Chamber of Commerce and Industry.
If confirmed, this would further undermine FIFA's stance.
The 56-year-old has denied any wrongdoing, however, insisting he will not resign from his post.
“I believe this allegation has something to do with my position in PSSI," he told iNews.
"I will not resign unless the voters [of PSSI] want me to."
Indonesia and Kuwait are the two nations currently banned from FIFA and were unable to vote in last month's Extraordinary Congress in Zurich last month when Gianni Infantino was elected to replace Sepp Blatter as President.