Football Federation of Burundi (FFB) vice-president Aimable Habimana has reportedly been arrested after bonuses meant for the team which participated in the Africa Cup of Nations allegedly disappeared.
The BBC reported Habimana was picked up for questioning relating to the missing money, due to be paid to the Burundi team that made its Africa Cup of Nations debut at the tournament in Egypt.
According to the BBC, the FFB vice-president has been detained since Saturday (July 6), along with two another unnamed officials from the governing body.
Further details have not been revealed regarding the case.
Burundi failed to score a goal or earn a point as they finished bottom of Group B.
Their 1-0 defeats to Nigeria and Madagascar were followed by a 2-0 loss at the hands of Guinea in their final group match.
The team has since headed home from the competition, due to conclude with the final on July 19.
But they have still not been paid overdue bonus from the tournament by the FFB, leading to the arrest of Habimana.
The incident marks the latest involving unpaid money meant for players competing at the Confederation of African Football's flagship event.
Nigeria's players boycotted a pre-match press conference and warned they might not to turn up for training over unpaid bonuses.
Cameroon had earlier threatened not to board their plane to Egypt owing to a similar row.
The crisis at the FFB marks an embarrassment for Burundi's International Olympic Committee and FIFA Council member Lydia Nsekera, who led the body from 2004 to 2013.