"We have found the Algerian plane. The wreck has been located ... 50 kilometres (30 miles) north of the Burkina Faso border" in the Malian region of Gossi, said General Gilbert Diendiere of the Burkina Faso army.
A witness had earlier reported seeing the plane "falling" in the region of Gossi and the general said they were taking the reports seriously as they matched radar images of the flight path.
"That is where we will strengthen our search," he had added.
The most likely cause of the crash is the weather, France's interior minister said on Friday, hours after the wreckage of the jet was found in Mali.
"We think that this plane crashed for reasons pertaining to meteorological conditions," Bernard Cazeneuve said on RTL radio, adding it was the "most probable hypothesis" although authorities were not excluding other potential causes for the accident of the jet, which had 51 French nationals on board.
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Flight AH5017, which originated in Ouagadougou and was bound for Algiers with 51 French nationals aboard, according to foreign minister Laurent Fabius, went missing amid reports of heavy storms, company sources and officials said.
It had been presumed to have been lost even before French President Francois Hollande went on TV to announce: "Everything leads us to believe that the plane has crashed."
He said the plane's Spanish crew had signalled they were altering course "due to particularly difficult weather conditions".
The French president's office said Friday the jet was clearly identified even though it had "disintegrated".
A "French military unit has been sent to (the area) to secure the site and gather evidence", it added in a statement.
President Francois Hollande expressed his solidarity with the families and friends of the victims.
Algerian Prime Minister Abdelmalek Sellal was earlier cited as saying by Algerian radio that the plane dropped off the radar at Gao, 500 kilometres (300 miles) from the Algerian border.
"Contact was lost with the McDonnell Douglas 83 at 1:47, a little after the pilots said they were diverting from the route due to meteorological reasons," Fabius had said.
The airline said it also had 24 Burkinabe, eight Lebanese, six Algerians, six Spanish, five Canadians, four Germans and two Luxembourg nationals on board.
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The MD-83 airplane that crashed was leased from Spanish company Swiftair. (Reuters file photo)
Mali, Algeria, Niger and France coordinated their search efforts under the umbrella of the French-led military intervention in Mali, Operation Serval.
"Even though the aircraft was above Mali it was in airspace managed by the control centre in Niamey in Niger," an air traffic control official told AFP.
Aviation sources told AFP the MD-83 was leased from Spanish company Swiftair.
Its six-member crew were all Spanish, said Spain's airline pilots' union Sepla, and Swiftair confirmed the aircraft went missing less than an hour after takeoff.
Suspected route of the flight
The plane had apparently been given the "all clear" following an inspection in France only this week, the French civil aviation authority DGAC said.
In France, two crisis units had been set up, at the DGAC and at the foreign ministry, DGAC said, in addition to another two at Roissy-Charles-de-Gaulle airport in Paris and at Marseille airport.
DGAC said that many passengers had been due to catch onward connecting flights to Paris and Marseille.
In Mali, the prime minister's office also said contact was lost around Gao.
"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," an airline source said.
"Contact was lost after the change of course."
The logo of the Air Algerie company office, at the Opera avenue in Paris. (AP photo)
A controller in Mali, also speaking on condition of anonymity, said the area was rocked by "strong storms" overnight.
Air Algerie, in a statement carried by national news agency APS, said it had initiated an "emergency plan" in the search for AH5017, which flies the four-hour passenger route four times a week.
In Cuba, the daughter of President Raul Castro assured journalists she was alive and well, contradicting reports that she had been onboard the doomed flight.
Mariela Castro, a sexologist and gay rights activist, said she had been told there was another passenger of the same name aboard flight AH5017. The crash comes less than six months after one of Algeria's worst air disasters.
In February, a C-130 military aircraft carrying 78 people crashed in poor weather in the mountainous northeast, killing more than 70 people.
The plane had been flying from the desert garrison town of Tamanrasset in Algeria's deep south to Constantine, 320 kilometres (200 miles) east of Algiers.
Tamanrasset was the site of the country's worst-ever civilian air disaster, in March 2003.
In that accident, all but one of the 103 people on board were killed when an Air Algerie Boeing 737-200 crashed on takeoff after one of its engines caught fire.
The sole survivor, a young Algerian soldier, was critically injured.