Contact with the Air Algerie flight was lost over the Sahara as it crossed Mali in bad weather, officials said.
French Foreign Minister Laurent Fabius said the plane, which has 50 French citizens aboard, "probably crashed".
French media later reported that soldiers had found wreckage in central Mali, but this has not been
confirmed.
Contact with Flight AH 5017, chartered from Spanish airline Swiftair, was lost about 50 minutes after take-off from Ouagadougou, Air Algerie said.
The pilot had contacted Niger's control tower in Niamey to change course because of a storm, officials say.
BBC West Africa correspondent Thomas Fessy says the route is well used by French travellers.
Speaking in Paris, Mr Fabius said:
"Despite intensive search efforts no trace of the aircraft has yet been found. The plane probably crashed."
He said French Mirage fighter planes were scouring the area.
Earlier, an Algerian official told Reuters that the plane had crashed, but gave no further details.
France's civil aviation body said crisis centres had been set up at airports in Paris and Marseille.
An Air Algerie spokesman quoted by Reuters said the provisional passenger list included 50 French
citizens, 24 people from Burkina Faso, eight Lebanese, four Algerians, two from Luxembourg, one Belgian, one Swiss, one Nigerian, one Cameroonian, one Ukrainian and one Romanian.
Officials in Lebanon, however, said there were at least 10 Lebanese citizens on the flight.
The six crew members are Spanish, according to the Spanish pilots' union.
"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), 500km (300 miles) from the Algerian border."
Burkina Faso Transport Minister Jean Bertin Ouedraogo said the plane sent its last message at around 01:30 GMT, asking air traffic controllers in Niger to change its route because of heavy rain.
In a statement (in Spanish), Swiftair said that the aircraft was an MD83 and that they were unable to establish contact with it.
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.
French Transport Minister Frederic Cuvillier told reporters that it was likely there were also many French nationals on board the plane.
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