There were few clear indications of what might have happened to the aircraft, or whether there were casualties, but Burkino Faso Transport Minister Jean Bertin Ouedrago said it asked to change route at 0138 GMT because of a storm in the area.
"I can confirm that it has crashed," the Algerian official told Reuters, declining to be identified or give any details about what had happened to the aircraft on its way north.
Air navigation services lost track of the MD-83 about 50 minutes after takeoff from Ouagadougou, the capital of Burkina Faso, at 0155 GMT (9:55 p.m. EDT Wednesday), the official Algerian news agency APS said.
The list of passengers includes 51 French, 27 Burkina Faso nationals, eight Lebanese, six Algerians, five Canadians, four Germans, two Luxemburg nationals, one Swiss, one Belgium, one Egyptian, one Ukrainian, one Nigerian, one Cameroonian and one Malian, Burkina Faso Transport Minister Jean Bertin Ouedraogo said. The six crew members are Spanish, according to the Spanish pilots' union.
The plane sent its last message around 0130 GMT (9:30 p.m. EDT), asking Niger air control to change its route because of heavy rains in the area, Ouedraogo said.
French Transport Minister Frederic Cuvillier said the plane vanished over northern Mali. He spoke Thursday from a crisis center set up in the French Foreign Ministry.
The plane had been missing for hours before the news was made public. It wasn't immediately clear why airline or government officials didn't make it public earlier.
Air Algerie Flight 5017 was being operated by Spanish airline Swiftair, the company said in a statement. The Spanish pilots' union said the plane belonged to Swiftair.
The flight path of the plane from Ouagadougou to Algiers wasn't immediately clear. Ouagadougou is in a nearly straight line south of Algiers, passing over Mali where unrest continues in the north.
Northern Mali fell under control of ethnic Tuareg separatists and then al-Qaida-linked Islamic extremists following a military coup in 2012. A French-led intervention last year scattered the extremists, but the Tuaregs have pushed back against the authority of the Bamako-based government.
A senior French official said it seems unlikely that fighters in Mali had the kind of weaponry that could shoot down a plane.
The official, not authorized to speak publicly, said on condition of anonymity that they primarily have shoulder-fired weapons — not enough to hit a passenger plane flying at cruising altitude.
Swiftair, a private Spanish airline, said the plane was carrying 110 passengers and six crew, and left Burkina Faso for Algiers at 0117 GMT Thursday (9:17 p.m. EDT Wednesday), but had not arrived at the scheduled time of 0510 GMT (1:10 a.m. EDT Thursday).
"In keeping with procedures, Air Algerie has launched its emergency plan," APS quoted the airline as saying.
The MD-83 is part of a series of long-range jets built since the early 1980s by McDonnell Douglas, a U.S. plane maker now owned by Boeing Co.