There were few clear indications of what might of happened to the aircraft, or whether there were casualties, but Burkino Faso Transport Minister Jean Bertin Ouedrago said it asked to change route at 01:38 GMT because of a storm in the area.
Algeria's state news agency APS said authorities lost contact with flight AH 5017 an hour after it took off from Burkina Faso, but other officials gave differing accounts of the times of contact, adding to confusion about the plane's fate.
Swiftair, the private Spanish company that owns the plane, confirmed it had lost contact with the MD-83 operated by Air Algerie, which it said was carrying 110 passengers and six crew.
A diplomat in the Malian capital Bamako said that the north of the country - which lies on the plane's likely flight path - was struck by a powerful sandstorm overnight.
Whatever the cause, another plane crash is likely to add to nerves in the industry after a Malaysia Airlines plane was downed over Ukraine last week, a TransAsia Airways crashed off Taiwan during a thunderstorm on Wednesday and airlines canceled flights into Tel Aviv due to the conflict in Gaza.
An Air Algerie representative in Burkina Faso, Kara Terki, told a news conference that all the passengers on the plane were in transit, either for Europe, the Middle East or Canada.
He said the passenger list included 50 French, 24 Burkinabe, eight Lebanese, four Algerians, two from Luxembourg, one Belgian, one Swiss, one Nigerian, one Cameroonian, one Ukrainian and one Romanian. Lebanese officials said there were at least 10 Lebanese citizens on the flight.
A spokeswoman for SEPLA, Spain’s pilots union, said the six crew were from Spain. She could not give any further details.
