The judge also issued arrest warrants for two other federation officials.
All three went voluntarily on Friday to speak with prosecutors after authorities froze their assets.
FIFA scandal deepens with 16 indicted for corruption
Chiriboga and another official were ordered to be held in house arrest, which is required by law because they are over 65, while the third was remanded into custody in prison.
Chiriboga has already been suspended by the soccer federation. His lawyer, Lucia Vallecilla, said prosecutors would have 90 days to review the finances of the federation as part of their investigation. She did not offer any further comment.
FIFA corruption case brings another wave of pre-dawn arrests
The heads of the associations that run soccer in North and Latin America, CONCACAF and CONMEBOL, and others with top jobs in the world governing body FIFA were among 16 people charged on Thursday on suspicion of bribery in connection with the sale of broadcast rights.
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