Burundi Football Federation (FFB) vice-president Aimable Habimana has been arrested over allegations of unpaid Africa Cup of Nations appearance bonuses.
BBC Swahili reported the funds, meant to be paid to the players for their tournament outings, is missing and Habimana, as well as two other FFB members, have been detained for questioning.
The Swallows appeared in their first ever Afcon finals, but failed to pick up a single point, losing 1-0 to Nigeria and Madagascar respectively, before going down 2-0 to Guinea in the final group match.
Burundi are not the only Afcon 2019-participating country to have battled with issues of player bonuses.
Nigeria's players refused to turn up for pre-match conference ahead of their group stage clash with Guinea, following complaints of unpaid match bonuses.