The incident - which also involved another helicopter - had “potentially catastrophic results,” an official probe has revealed.
The JS41 Jetstream airplane narrowly avoided the S92 helicopter in the near miss on September 23, 2013.
The airplane flew less than 500ft over the helicopter after aborting its landing.
The pilot of the Jetstream assessed the risk of a collision between the aircraft as “high” - but the S92 pilot claimed there was no risk of a crash.
The UK Airprox Board, which investigates near misses, “concluded that this incident displayed the classic hallmarks of the holes in the many available safety barriers aligning to result in an unfortunate final outcome”.
The Jetstream was on final approach to land at Aberdeen International Airport with a helicopter on the runway ahead.
The aerodrome controller instructed the helicopter to take off and cleared the Jetstream for landing as the chopper left the runway.
However, as the pilot of the Jetstream was preparing to land another helicopter became visible a short distance from the plane.
The Jetstream pilot immediately aborted the landing and pulled up, flying less than 500ft over the S92.
As the airplane climbed away from the airport, the Jetstream pilot became aware of the first helicopter flying a short distance ahead.
The pilot turned 270 degrees right to avoid the helicopter and resumed climbing, before being directed back to the airport for a normal landing.
UK Airprox Board assessors reported that the pilot of the S92 had read back an instruction which had been issued to the pilot of another helicopter.
The mistake was missed because the pilot’s read back was blocked by another transmission and the controller was not aware the S92 was on the runway.
UKAB members concluded the incident was caused by the pilot of the S92 lining up on the runway without clearance.
The problem was contributed to by the aerodrome controller failing to see the S92 during a visual check and cleared the Jetstream to land.
The incident was graded as C - an alert in where aircraft were in close proximity but no risk of collision existed.
Aberdeen International Airport has been advised to take steps to prevent a similar incident in the future.
“When discussing the cause of the Airprox, the Board quickly decided that the main factor was that the S92 pilot, albeit unintentionally, entered the runway without a clearance,” said the report.
“The National Air Traffic Services advisor stated that, when the Jetstream had actually passed the S92, it was estimated by ATC to be about 400-500ft above the helicopter.
“By this time the S92 pilot had vacated the runway. Although it was realised that in other circumstances this could have been a very serious incident, the Board therefore considered that the actual risk of collision in this case was Category C because the pilots concerned had taken effective and timely action to prevent the aircraft colliding.”