Senegal's civil aviation authority said the craft and a much bigger commercial jet may have "touched" in mid-air, while a local media outlet said the smaller plane was believed to have run out of fuel.
The HS125 twin-engine plane, belonging to the company Senegalair, was flying from Burkina Faso to Dakar with a crew of three, three medical workers and a French patient.
It disappeared from radars shortly after 7 pm local time yesterday over the Atlantic, 111 kilometres west of the Senegalese capital, Senegal's civil aviation authority Anacim said in a statement.
"Initial information suggest the two aircraft may have touched," it said. "A technical investigation will provide confirmation, or refutation, of this." The Ceiba flight, which was heading to the Benin capital of Cotonou, was re-routed to Malabo, the airline's main hub, it said.
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Senegal's Futurs Medias news group reported that the medical aircraft was suspected of having run out of fuel.
Senegal's air force was searching the area for signs of the plane, according to airport sources in Burkina Faso.
Apart from the female French patient, the plane was carrying two Senegalese nurses and a Senegalese doctor as well as a Congolese man and two Algerian crew members.
Contacted by AFP, France's foreign ministry declined to reveal the identity of the French patient who was being airlifted, nor the reason for the person's presence in Ouagadougou.
Officials did say the French embassy in Dakar was in contact with the patient's family.