Air navigation services lost track of the MD-83 about 50 minutes after takeoff from Ouagadougou, the capital of Burkina Faso, at 0725 IST, the official Algerian news agency APS said.
French Foreign Minister Laurent Fabius said Air Algerie Flight 5017 had "probably crashed." Fabius said "no trace" of the plane had been found.
Two French fighter jets are among aircraft scouring the rugged north of Mali for the plane, which was traveling from Burkina Faso's capital, Ouagadougou, to Algiers, the Algerian capital.
The flight was being operated by Spanish airline Swiftair, the company said in a statement. The Spanish pilots' union said the plane belonged to Swiftair.
The plane sent its last message around 0700 IST, asking Niger air control to change its route because of heavy rains in the area, Burkina Faso Transport Minister Jean Bertin Ouedraogo said.
The disappearance of the Air Algerie plane comes after a spate of aviation disasters.
Fliers around the globe have been on edge ever since Malaysia Airlines Flight 370 disappeared in March on its way to Beijing. Searchers have yet to find a single piece of wreckage from the jet with 239 people on board.
Nothing indicates the jet was the target, but two back-to-back disasters involving Boeing 777s flown by the same airline was too much of a coincidence for many fliers.
Then this week, US and European airlines started canceling flights to Tel Aviv after a rocket landed near the city's airport.
Finally, yesterday, a Taiwanese plane crashed during a storm, killing 48 people.
It's easy to see why fliers are jittery, but air travel is relatively safe.
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