Utah Valley University student Luke Tait shot the video Friday while waiting in a security line. It has been viewed on YouTube more than 765,000 times.
Tait said the boy appeared so shy he couldn't keep his arms raised for a pat-down, and the father removed his son's shirt out of frustration to speed up the search.
"I was shocked and realized something crazy was going on, so I took my BlackBerry off the conveyor belt and started recording," Tait told The Associated Press on Monday from Oxford, Miss., where he traveled for Thanksgiving.
"A couple of times the father raised the arms of the boy. That ended up not being enough, so the father got frustrated and tore his boy's shirt off," Tait said.
That prompted a security officer to protest, "Sir, sir!"
The Transportation Security Administration said in a blog posting that nobody has to de-robe at an airport checkpoint. Passengers need only remove shoes, coats and jackets for a screening.
The boy was being searched because he sounded an alarm inside a metal detector, the TSA said. The boy's father removed his son's shirt to expedite the screening.
"That's it. No complaints were filed and the father was standing by his son for the entire procedure," said the posting by "Blogger Bob" of the TSA Blog Team.
Dwayne Baird, a regional public affairs manager for TSA, didn't immediately return messages from the AP on Monday. Another message was left at the public-affairs unit of TSA headquarters in Washington.
Tait said he never learned the identity of the boy or his father. He tried to approach the pair but said he was stopped by a man in a dark suit who appeared to be a TSA supervisor "grilling me about my motives."
Tait said the man demanded he delete his video, but he refused. He said he was followed by four TSA agents to his gate but allowed to board a plane without further questioning.