"We can confirm that the qualifying match between Mali and Algeria will be played on neutral ground," a spokesman said.
It followed a request from Algeria to move the game because of fears for the safety of their team following the March military coup in Mali, the Taureg uprising in the north of the country and recent insurrection within the army in Bamako.
The match will still be played on June 9, but now in Ouagadougou, Burkina Faso, according to a statement from the Mali Football Federation but not yet confirmed by FIFA.
Algeria host Rwanda in their opening Group H match at Blida on Saturday while Mali, whose French coach Alain Giresse recently quit following the uprising in Bamako, are away at Benin on Sunday.
FIFA has told Libya they must host their World Cup Group I qualifier against Cameroon in neutral territory. It will be played behind closed doors in the Tunisian coastal town of Sfax.