A near-collision, or "airprox", incident occurred on average almost once a fortnight in the last 15 years - despite a safety device being recommended but never fitted.
At least 46 of these were the most dangerous Category A - where a risk of an actual collision occurred - and eight involved two Tornados. In July 2012 two Tornado jets crashed into one another over the Moray Firth, claiming the lives of three crew.
Last night SNP defence spokesman and Westminster leader Angus Robertson, who obtained the figures, said: "These statistics on aircraft near-collisions are truly shocking.
"What stands out are the 361 incidents involving RAF Tornado jets - of which at least 46 were the most dangerous 'Risk Category A' where a risk of an actual collision occurred - and, of those, at least eight were incidents involving two Tornados. Almost all aircraft types have collision-avoidance systems to reduce the risk, but RAF Tornados, which are involved the most in near-collisions, do not.
"Fast jets and their crews face particular training and operational risks, but the MoD has a duty of care to provide potential life-saving equipment like collision-warning systems."
He added: "Such a system was recommended by the MoD in 1998 for Tornados but have not yet been installed.
"Tragically, two Tornados from RAF Lossiemouth collided above the Moray Firth in 2012 killing three personnel and seriously injuring a fourth.
"We will learn shortly whether a Fatal Accident Inquiry will be held and no doubt the absence of a collision-warning system will be part of the considerations".
Squadron Leader Sam Bailey, 35, and Flight Lieutenants Hywel Poole, 28, and Adam Sanders, 27, died when the Tornados collided.
Since 1998, there have been 361 airprox near-misses involving Tornados, according to statistics from the MoD and the Civil Aviation Authority UK Airprox Board.
The collision-avoidance system was first recommended as part of a 1998 Strategic Defence and Security Review.
Its introduction was delayed, and aircraft will finally be fitted with the devices next year.
The figures, which include all near misses across the UK, cover the period during which Tornados had their main operating bases at RAF Lossiemouth, RAF Leuchars in Fife and RAF Marham.
An MoD spokesman said: "Air proximity incidents are extremely rare in comparison to the millions of flights in UK air space every year.
"Tornado pilots, like all military aviators, have multiple mitigation measures in place that reduce the risks of mid-air collisions."
He added: "There are already a range of mitigation measures in place to minimise the risk of mid-air collision and tragic incidents, such as that in Moray, are extremely rare.
"A specifically designed Tornado Collision Warning System, which will be another tool for pilots, is currently being trialled and will be in service in next year."
l One of the RAF's oldest squadrons is to be transferred from Norfolk to Lossiemouth.
Number II (Army Co-operation) Squadron, based at RAF Marham, will move to RAF Lossiemouth in Moray in 2015.
The unit marked 100 years' service in 2012 and is currently training for its next tour of duty in Afghanistan.
On its return the squadron will swap Tornados for the latest Eurofighter Typhoons to make the move north.