The flight with 116 passengers aboard was on its way from Burkina Faso to the Algerian capital when it disappeared from the radar.
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.
More than 50 French were onboard the plane along with 27 Burkina Faso nationals and passengers from a dozen other countries. The flight crew was Spanish.
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 0130 GMT (9:30 p.m. EDT), 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.
Last week, a Malaysia Airlines flight was shot down by a surface-to-air missile while flying over a war-torn section of Ukraine. 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, U.S. and European airlines started canceling flights to Tel Aviv after a rocket landed near the city's airport. Finally, on Wednesday, 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.
There have been two deaths for every 100 million passengers on commercial flights in the last decade, excluding acts of terrorism. Travelers are much more likely to die driving to the airport than stepping on a plane. There are more than 30,000 motor-vehicle deaths in the U.S. each year, a mortality rate eight times greater than that in planes.
French Transport Minister Frederic Cuvillier said the Air Algerie flight vanished over northern Mali. He spoke Thursday from a crisis center set up in the French Foreign Ministry. Cuvillier didn't specify exactly where the plane disappeared over Mali, or whether it was in an area controlled by rebels.
But Algerian Prime Minister Abdelmalek Sellal said on Algerian state television said that 10 minutes before disappearing, it was in contact with air traffic controllers in Gao, a city essentially under the control of the Malian government, though it has seen lingering separatist violence.
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.
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).
Swiftair said it has not been possible to make contact with the plane and was trying to ascertain what had happened. It said the crew included two pilots and four cabin staff.
"In keeping with procedures, Air Algerie has launched its emergency plan," APS quoted the airline as saying.
Algerian aircraft were overflying the region around Gao to try to locate wreckage, said Houaoui Zoheir, spokesman for the Algerian crisis center. He provided no details on the type or number of aircraft.
"As long as we haven't found the wreckage, we can't talk of a crash," he said. "We talk of loss of contact."
The passengers include 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, Ouedraogo said. The six crew members are Spanish, according to the Spanish pilots' union.
The MD-83 is part of a series of jets built since the early 1980s by McDonnell Douglas, a U.S. plane maker now owned by Boeing Co. The MD-80s were the workhorse of domestic air travel in the U.S. and are used for a flights of a few hours over land elsewhere.