The wreckage was spotted in the Gao region, where "investigations continue", Algeria's Minister of Public Works Amar Ghoul said.
Air Algerie Flight AH5017 took off from Ouagadougou, Burkina Faso, bound for Algiers carrying 110 passengers, at least 50 of them French nationals, and an all-Spanish crew of six.
Though the flight was operated by Air Algerie, the plane belonged to Spain-based charter company Swiftair, which said radar contact with the MD-83 aircraft was lost 50 minutes after takeoff from the capital of Burkina Faso.
"Everything allows us to believe this plane crashed in Mali," French President François Hollande said after a meeting in Paris with top officials.
The crew changed course due to "particularly difficult weather conditions", he said.
"All military means we have in Mali" would be mobilised in the search for the missing airliner, Hollande said.
France still has a significant military presence in Mali after a January 2013 intervention to battle Muslim militants who seized control of the northern part of the country.
What appeared to be parts of the missing plane were found near the city of Gossi, Malian police sources told Efe news agency.
The zone where the possible wreckage was spotted lies near an area where jihadi groups have been active lately and their presence could pose an obstacle to search and recovery efforts.
Spanish Foreign Minister Jose Manuel Garcia-Margallo extended offers of technical support to the governments of Algeria and Mali.
Garcia-Margallo, who was making a previously scheduled official visit to Tunisia, contacted his Algerian and Malian counterparts and remained in constant touch with Spanish Prime Minister Mariano Rajoy, sources at the foreign ministry in Madrid told Efe.