They were asked to retrace their steps through security at Izmir airport in Turkey for extra checks sparked by claims made by fellow passengers on the Thomas Cook airline's Manchester-bound plane last week, the Manchester Evening News reported.
Thomas Cook airline apologised to the passengers who came under suspicion after two female passengers told cabin crew that they had witnessed the men "skipping security scanners" and signalling to each other while aboard the plane.
They returned to the terminal to re-do security checks, and were eventually given the all clear to travel.
But the incident that took place on Wednesday meant the flight was delayed by nearly 90 minutes.
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When the men were finally allowed to re-board, their accusers -- who also alleged they were "making phone calls" -- refused to travel with them, instead choosing to return to the terminal.
As the drama unfolded just before take-off, fellow passengers said they were shocked.
"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," the passenger was quoted as saying.
It is understood that 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, the report said.
They complained about the men "making gestures to each other" and "going to the toilet to use their phones", it said.
The men, who were said to remain calm throughout despite the accusations, were then given the all-clear.
A spokesman for the Thomas Cook Airlines, was quoted as saying, "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," he said.