Bolivia Football Federation (FBF) president Charlos Chavez was arrested on Saturday as part of a corruption inquiry.
Chavez is also the treasurer of the South American Football Confederation (CONMEBOL), reports bbc.com.
The country began probing its football federation after the major corruption scandal that hit world football governing body, FIFA in May. More than 20 Bolivian football executives have given evidence in the courts so far.
Chavez has been accused of "alleged corruption in the management of resources", Bolivia's public prosecutor said.
The secretary general of the Bolivian federation, Alberto Lozada, was also taken into custody for fixing games.
FIFA is facing a lot of criticism of late after Swiss police raided a hotel in Zurich and arrested seven of its top executives in May.
Two former CONMEBOL presidents, Eugenio Figueredo and Nicolas Leoz, are among those charged.
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