The man agreed to go through normal metal detectors at San Diego airport but refused to submit to one of the new full-body scans.
He says he was threatened by security guards as a result.
His mobile phone footage of the incident - dubbed 'Don't touch my junk' - has become a web sensation.
John Tyner, 31, left his mobile phone recording video and sound as he pulled off his shoes and as his carry-on items were screened at airport security.
He was pulled out of the line for the standard metal detector and was asked instead to go through one of the newly installed body scanners, called Advanced Imagery Technology units or AITs.
His phone was still recording as he refused on privacy and health grounds and was instead sent for one of the new pat-downs.
"We're going to be doing a groin check. That means I'm going to place my hand on your hip, my other hand on your inner thigh, slowly go up, and slide down," a security worker says in the clip.
"We are going to do that two times in the front and two times in the back.
"And if you'd like a private screening, we can make that available for you also."
Mr Tyner responded: "We can do that out here, but if you touch my junk, I'm going to have you arrested."
A supervisor was then called, who said: "If you're not comfortable with that we can escort you back out and you don't have to fly today."
"OK, I don't understand how a sexual assault be made a condition of me flying," Mr Tyner said.
In the end Mr Tyner's ticket is refunded and he leaves but not before being confronted by security officials.
He says one of the security officials told him he could face charges and a fine of $10,000.
"I would like to leave now. If I'm free to go I would like to leave," Mr Tyner said.
"All I'm trying to do is get you to cooperate," the security guard said.
"It would look better for you when we bring the case against you that we are going to bring ... that you cooperated."
Mr Tyner says his video was not a set up and he will not be flying again anytime soon.
Hundreds of the full-body scanners are being installed around US airports.
America's Transport and Security Administration says all passengers must be screened and the new measures are a response, in part, to the notorious underwear bomber incident on a flight to Detroit last Christmas.
"They in no way [are] electronic strip searches," homeland security secretary Janet Napolitano said.
"All they do is ping in a private area, away from the gate, with an image that is neither retained nor transmitted."
With the busy holiday season approaching, the Airline Pilots Association has voiced its concern about the pat-downs and tourism groups are reporting an increase in traveller complaints.
"We have an open ear, we will listen - it's all about everybody recognising their role," Ms Napolitano said.
US transport officials point to surveys showing a majority of passengers approve of the new procedures.
abc.net.au
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