Since the Eurofighter plane involved lost an outer fuel tank in the collision, said the air force, it would suggest the civilian jet had simply flown too close to it from below.
"Of course we want to wait for the conclusive report, but it will run along these lines," an air force spokesman said in Berlin on Wednesday, partially confirming earlier press reports.
Prosecutors said on Tuesday that they had launched investigations into pilots of the second and third aircraft - both Eurofighter fighters - for involuntary manslaughter.
But the airforce's theory is "pure speculation, one of many possible variations," said the German Federal Bureau of Aviation Accident Investigation (BFU) on Wednesday.
The crashed civilian plane's black box recorder has been found and is now being examined by prosecutors in Cologne.
Investigators also hope radar recordings from German air traffic control can shed light on the incident and have examined the damaged Eurofighter, which made it back to base.
Earlier reports in Spiegel Online and Süddeutsche Zeitung suggested the civilian Learjet had rammed the Eurofighter from below in a sharp left curve.
The reports, citing inside sources familiar with the investigation, said the Learjet pilot is thought to have made a “fatal error”.
Two people onboard the aircraft, both ex-military pilots aged 43 and 50, are thought to have been killed in the crash.
Body parts were reported found at the crash scene, which have not yet been identified.
The civilian craft, on loan to the military, crashed after colliding with a fighter jet during a simulation exercise on Monday afternoon, 2,500 metres above the town of Olsberg-Elpe in the Sauerland region of western Germany.
Officials said the exercise had been to simulate conditions where an unknown aircraft enters German airspace without identifying itself via radio and must be lead to a safe landing spot by a military plane.
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