John Blakeley, who previously presided over RAF Boards of Inquiry into accidents, also said a fault involving the Chinook's Full Authority Digital Engine Control (Fadec) computer system was at least as likely as pilot error to have been a cause of the notorious crash of a Mk2 on the Mull of Kintyre in Scotland in 1994.
The helicopter's two pilots were blamed for the crash, which killed all 29 on board, including 25 senior police and intelligence officers.
Blakeley is the most senior RAF engineering officer to question the decision to blame the pilots.
He said, "A scenario such as an intermittent defect in the engine control system was more plausible, by the number of facts supporting it, than an aircrew error accident."
He has made his comments - for the first time in public - in a 19-page review of the airworthiness, engineering and maintenance aspects of the board of inquiry into the accident involving Chinook ZD576.
The publication of his report this week comes as the families of those who died in the crash mark the 10th anniversary of the accident, which happened on 2 June 1994.
Computer Weekly has campaigned for the government to hold a new inquiry into the accident after the RAF accused the pilots of ZD576, flight lieutenants Rick Cook and Jonathan Tapper, of being grossly negligent.
The verdict was despite evidence to an RAF Board of Inquiry, which investigated the accident, that problems with the Chinook Mk2's Fadec system had led to incidents of a "flight-critical nature". Engines shut down or surged without pilot command, and spurious engine warning lights appeared in the cockpit.
Blakeley, who was asked to conduct his review by the father of one of the pilots, said in his report that the RAF appears to have made an "immediate presumption" of pilot error after the accident. It did not deviate from this position "even when witness evidence might have questioned this approach".
He said the focus in the accident investigation on the pilots avoided addressing some "very basic and very difficult to answer questions raised on the airworthiness" of the Chinook Mk2 aircraft, "and ZD576, in particular at the time of the accident".
Blakeley questioned why the RAF was operating the Chinook Mk2 "at all at this time". He also said that aspects of the technical and engineering evidence around the crash were never fully analysed by the RAF.
Blakeley said he did not know the cause of the crash but found that a jamming of the controls or an engine surge "as likely, if not a more likely," scenario as "gross negligence". He said he found it incredible that the RAF made no "no serious attempt to see if a technical problem could have fitted the same accident scenario" as pilot error.
But he said that technical malfunction as a cause of the crash would raise uncomfortable questions about the decision to put the Chinook Mk2 into service. These issues would be "even today" an embarrassment to the Ministry of Defence, he said.
The RAF had become so used to a "significant number of unexplained and sometimes flight safety-related incidents" that it was "no longer questioning the underlying airworthiness of the aircraft" said Blakeley.
Defence standard JSP 318 defined airworthiness as the ability of an aircraft or other airborne equipment or system to operate without significant hazard to aircrew, groundcrew, passengers (where relevant) or to the general public over which the airborne systems are flown. Blakeley said the problems experienced by pilots of Chinook Mk2 show the aircraft "could hardly have been seen as fully compatible with meeting the JSP definition of airworthiness".
An Mod spokesman said, "In the 10 years since this tragic accident the MoD has examined all of the complex technical legal and airmanship issues raised by those opposed to the board of inquiry's finding but has found nothing to undermine it."