A flight operated by Air Algérie carrying 116 people from Burkina Faso to Algeria disappeared from radar during a sandstorm early on Thursday, the plane's owner and Algerian officials said as a three-country search for the plane began.

Air traffic controllers lost contact with the Swiftair-owned MD-83 about 50 minutes after takeoff at 1.17am local time (0117GMT), said an Algerian aviation official. The news was not made public until several hours after the flight's scheduled 5.10am arrival in Algiers, by which time officials from Algeria, Burkina Faso and France – which had 50 nationals aboard – issued conflicting details.

The flight path of the plane from Burkina Faso's capital, Ouagadougou, was not immediately clear. The city is in a nearly straight line south of Algiers, passing over Mali, where unrest continues. Rebels who have seized the northern fringe of Mali do not have weapons capable of bringing down a commercial jet at cruising altitude, a Malian official told the Guardian. "What they have is shoulder-fired weapons, and rocket-propelled grenades."

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The flight had asked to change route at 1.38am because of a storm, Burkina Faso's transport authorities said. Powerful sandstorms are frequent throughout the Sahara's northern belt around this time of the year. Aviation officials in Burkina said they handed the flight to a control tower in Niger's capital, Niamey, at 1.38am, and that last contact was about 4.30am. That contradicted an Algerian aviation official, who said the last contact was at 0155 GMT when the plane was flying over Gao, Mali.

Issa Saly Maiga, head of Mali's National Civil Aviation Agency, said a search was under way. "We do not know if the plane is in Malian territory," he told Reuters. "Aviation authorities are mobilised in all the countries concerned – Burkina Faso, Mali, Niger, Algeria and even Spain."

Swiftair said the company was trying to ascertain what had happened. A crisis unit has been set up in Ouagadougou airport. The flight manifest includes 50 French nationals, while the six crew members are Spanish.