Two men were removed from a plane heading for Manchester and made to go back through security after other passengers claimed they were making gestures on board.
The female passengers told cabin crew they saw the men skipping security scanners and signalling to each other on the plane, which was flying to Manchester Airport from Turkey.
Thomas Cook has now apologised to the men, who had to get off the flight just before take off, reports the Manchester Evening News.
They went back to do security checks and were given the all clear to travel service MT685 from Izmir to Manchester on Wednesday afternoon.
The incident meant the flight - and all other passengers - were delayed by 90 minutes.
And the two women who reported them refused to fly - returning to the terminal instead.
Other passengers reported feeling shocked, with one saying it was an embarrassment.
The woman, who asked not to be named, said: "Two innocent Muslim men were marched off the plane and searched as two English ladies refused to fly with them on the plane.
“The result was a delay for everyone and the men flew, while the women were left behind.”
It’s understood the two men were in their seats and preparing for take-off when two women chose to complain to Thomas Cook cabin crew about them.
It's understood they complained about the men ‘making gestures to each other’ and ‘going to the toilet to use their phones’.
The women were also said to have alleged the men had ‘missed the security scanners’, leading cabin crew to ask them if they could retrace their steps through the terminal.
The men, who were said to remain calm throughout despite the accusations, were then given the all-clear.
A spokesman for Thomas Cook Airlines, said: “Two customers on this flight were asked to go through security a second time as a precaution, after unverified concerns were raised that the initial airport security check had missed them out.
“We’d like to thank these two customers for their patience and apologise for any inconvenience."