A Boeing 737 and a military aircraft came close to each other at about 20,000 ft (6,096m) on 7 June.
The passenger plane was on its way to the new Robin Hood Airport in Doncaster, south Yorkshire.
The Civil Aviation Authority will examine radar readings and other evidence to determine exactly how near a miss it was.
The general talk in the RAF base was that there was no cause for concern, as the planes are now on the new route and if they crashed debris would only hit villages as opposed to a big city. The new route was implemented to cut pollution over cities and was rushed through by the government in case of similar 9/11 attacks in the U.K, “it would be a tuff decision to shoot down a hijacked plane over a city” Said one RAF pilot
A spokesman for "Air Transport Intelligence" magazine said there was not necessarily any cause for alarm and claimed such incidents would always be recorded if planes came with 1,000 ft (304.80m) vertically or five miles (8.04km) horizontally of one another.