Contact was lost about 50 minutes after take-off from Ouagadougou, it said. The plane was last seen at 0155 GMT.
Flight AH 5017 had 110 passengers and six crew on board, Spanish airline Swiftair, which owns the plane, said.
The pilot had contacted Niger's control tower in Niamey to change course because of a storm, correspondents say.
Algerian and French nationals are thought to be on board.
"In keeping with procedures, Air Algerie has launched its emergency plan," Air Algerie officials, quoted by APS news agency (in French), said.
Algerian Prime Minister Abdelmalek Sellal reportedly told Algerian radio: "The plane disappeared at Gao (in Mali), 500 kilometres (300 miles) from the Algerian border."
UN troops in Mali say they understand the plane came down between Gao and Tessalit, the BBC's Alex Duval Smith in the Malian capital Bamako reports.
Brigadier General Koko Essien, who is leading the UN troops, told the BBC that the area leading up to the Algerian border was vast and sparsely populated.
He added that weather in the area had been bad overnight.
Armed groups are also said to be active in the area. However, at the moment the most probable scenario looks like a plane that came down in bad weather, our correspondent adds.
The plane is operated by Air Algerie and chartered from Swiftair.
In a statement (in Spanish), Swiftair said that the aircraft was an MD83 and that they were unable to establish contact with the plane.
An Algerian official had previously told Reuters that the plane was an Airbus A320.
An unnamed Air Algerie company source, speaking to AFP news agency, said: "The plane was not far from the Algerian frontier when the crew was asked to make a detour because of poor visibility and to prevent the risk of collision with another aircraft on the Algiers-Bamako route."
"Contact was lost after the change of course."
Flight AH 5017 flies the Ouagadougou-Algiers route four times a week, AFP reported.
Algerian nationals were among those on board, Algerian newspaper Ennahar reported.
French Transport Minister Frederic Cuvillier told reporters that it was likely there were also many French nationals on board the plane.
In February a military plane in Algeria crashed, killing 77 people on board.
The Hercules C-130 crashed into a mountain in Oum al-Bouaghi province, en route to Constantine, in bad weather conditions. Only one person on board survived.
Source: BBC News
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