The pilots had sent a final message to ask Niger air control to change its route because of heavy rain, Burkina Faso Transport Minister Jean Bertin Ouedraogo said Thursday.
The vast deserts and mountains of northern Mali fell under control of ethnic Tuareg separatists and then al-Qaida-linked Islamic extremists after a military coup in 2012.
French forces intervened in January 2013 to rout Islamist extremists controlling the region. A French soldier was killed earlier this month near the major town of Gao, where French troops remain.