The data also reveals passengers flying from Edinburgh suffered the third worst UK airport delays in June, which averaged 26 minutes and were more than twice as long as pre-pandemic.
The report from aviation analytics firm Cirium showed cancellations are having a greater impact on travel because airlines are operating around one quarter fewer flights than in 2019.
It said the proportion of flights cancelled at short notice (fewer than three days) had increased to 3 per cent at Glasgow Airport in June compared to 1 per cent in June 2019.
At Edinburgh, the figure increased from 0.8 per cent to 2.3 per cent.
Aberdeen’s figure went up from 1.7 per cent to 2.4 per cent.
Inverness’s fell from 2.7 per cent to 2.2 per cent.
However, Scotland fared better than some English airports.
Southampton experienced 6.4 per cent late notice cancellations in June, with 6.2 per cent at London City and 4.8 per cent at Bristol.
Gatwick had the highest number of such cancellations, such as some of Easyjet’s, which accounted for 3.9 per cent of the airport’s flights.
Heathrow – the UK’s busiest airport – had the second highest number and was 2.2 per cent of the airport’s total flights.
The staff shortages have been attributed to an exodus from aviation after pandemic lockdowns grounded most flights and the industry was no longer seen as secure employment.
There have also been enduring Covid fears about working close to large numbers of people, and delays in security vetting for airline and airport jobs.
Average departure delays at Edinburgh Airport in June increased to 26 minutes compared to 12 minutes in June 2019.
The 116 per cent increase compares to a UK average rise of 71 per cent.
Glasgow’s average – the UK’s fifth highest – was up from 15 to 21 minutes.
Aberdeen’s increased from eight to 14 minutes, while Inverness’s was up from nine to 12 minutes.
Only Gatwick and Bristol had longer average delays than Edinburgh, of 34 and 30 minutes respectively.
Heathrow’s was 25 minutes, while Southampton’s was one minute.
Cirium’s figures were for the UK’s 28 busiest airports, with the data based on flights departing the UK only.
A spokesman for Edinburgh Airport said: “The whole aviation industry continues to be impacted by the tumultuous shock caused by Covid.
"The data does not provide context.
"Aviation was one of the first industries to feel the impact of the pandemic and will be one of the last to recover.
"It was subject to some of the tightest restrictions imposed by governments, resulting in thousands of jobs being lost.
"Considering restrictions were only lifted at the end of March, it is unrealistic to think any industry could recover to pre-pandemic levels in a matter of months.”
A spokesperson for AGS Airports, which owns Aberdeen, Glasgow and Southampton, said: “What these figures clearly show is our airports aren’t experiencing the same level of disruption as elsewhere.
"The industry as a whole has been facing a number of challenges which has resulted in airlines having to regrettably cancel a number of flights.”