A senior RAF officer threatened to "break the f****** legs" of a pilot if he told anyone about the findings of an inquiry, a court heard.
The allegation, made by Flight Lieutenant Andrew Townshend, relates to a military passenger jet that suddenly went into a nosedive while he was in command.
The Voyager plane, with nearly 200 personnel on board, plummeted when he lost control after his digital camera jammed the flight controls.
The Nikon digital camera Flt Lt Townshend, 49, had allegedly been using in the cockpit to take pictures of passing aircraft caused the autopilot to disengage.
The incident took place over the Black Sea during a flight from RAF Brize Norton to Camp Bastion in Afghanistan on February 9th, 2014.
Many of the crew and passengers thought they were going to die when the aircraft plummeted 4,400ft in a matter of seconds.
Flt Lt Townshend is facing a court martial in Bulford, Wiltshire, accused of lying in both a technical log and service inquiry, insisting the incident had been caused by a technical fault.
He denies two counts of perjury and making a false record in relation to lying but admits negligently performing a duty in relation to the camera colliding with the aircraft's control stick.
Following the incident a service inquiry, led by Group Captain Timothy Jones, was set up to find out what happened.
Within a few weeks, the service inquiry had ruled out a technical fault with the Voyager jet and instead believed Flt Lt Townshend's camera had been the cause.
The court has previously heard the defendant's co-pilot, Flight Lieutenant Nathan Jones, say he was told the reason for the incident by the service inquiry panel and was then threatened to keep quiet.
Flt Lt Jones alleged Squadron Leader Nathan Giles, from the Military Air Accident Investigation Branch, switched off the tape, grabbed him by the collar and said:
"If you tell anyone about this I will break your f****** legs'."
John Price QC, defending Flt Lt Townshend, suggested to Gp Capt Jones that Sqn Ldr Giles had said the same thing to his client.
"Flt Lt Townshend maintains that Squadron Leader Giles said the same thing to him - 'tell anybody, I'll break your f****** legs'," Mr Price said.
The witness replied: "I wasn't aware of that."
Mr Price said Flt Lt Townshend was "very upset" at the suggestion during one of his interviews with the service inquiry that he was lying.
Gp Capt Jones replied:
"I think I took a different view. Some of the interviews were difficult and tense."
"That is because we were putting evidence before Flt Lt Townshend that didn't match hitherto what he had told us.
"You say that we were accusing him of lying and here we were as a service inquiry panel with compelling evidence of physical manipulation of the stick by the camera and the only person who could explain that was Flt Lt Townshend."
"He would say that cannot be true because that would mean he would be a liar. He said he couldn't think of a reason why it had occurred but he said he couldn't remember."
Gp Capt Jones added:
"What was happening in those interviews was that we were giving a factual explanation of evidence and asking him to explain it and that's why he reacted in the way he did."
The court martial was adjourned.