The MD-83 twin-engine plane lost radar contact 50 minutes after departure from the Ouagadougou airport during what was expected to be a four hour flight into Algiers' Houari Boumediene Airport.
Swiftair, a private company that operates Air Algerie, confirmed: "We have lost contact with the plane," and that "At this moment, emergency services and our staff are working on finding out more on this situation."
It is possible the plane crashed as it flew over Mali. United Nations troops in Mali told the BBC the plane possibly crashed between Gao and Tessalit, in an area that Brigadier General Koko Essien described as remote. The weather at the time, he said, was severe.
The 116 aboard includes 110 passengers, two pilots, and four crew members.
Air Algerie noted via Twitter that 50 of the passengers were French.