Aimable Habimana has been placed under arrest since Saturday.
The vice-president of the Burundian football association, FFB, has been arrested pending an investigation after the apparent disappearance of bonus money for the national team players who were recently in Egypt for the Africa Cup of Nations finals.
The BBC understands that Aimable Habimana, also known as Marandura, has been placed under arrest since Saturday.
The BBC has tried to speak to the Burundian police without success, but a member of the Burundian FA, who preferred to stay anonymous, confirmed the story.
The same person said that Mr Habimana was arrested together with two other employees while investigations are being carried out.
Burundi, which was taking part in its first Afcon finals, were eliminated in the group stage.