The 39 second clip, shot on a cell phone camera at Salt Lake International Airport on Friday, shows a young boy with his shirt off and TSA officials patting him down.
The video was posted on YouTube by Luke Tait, a University of Utah student.
Tait told CNN "The father kind of assisted a little bit and he stood by his son and kind of held his arms out, trying to help the TSA agent kind of perform the pat down, he did that actually twice."
Tait said it's not clear exactly what led TSA officials to pat-down the kid.
TSA spokesman Dwayne Baird told CNN the screeners searched the child after he set off a metal detector alarm.
"The father got a little upset and he tore his son's shirt off and gave it to the TSA agent and at this time, that's when the TSA agent was yelling 'Sir, sir' at the man, the father of the kid," Tait said.
The clip has generated hundreds of thousands of hits on YouTube .
Congressman Jason Chaffets (R-Utah) said it is important to know all the facts before people rush to judgement, but said it was clear that the TSA crossed the line.
"Between the whole body imaging and the pat downs and kids having to take their shirts off it just seems like we're going a little too far."
Asked about the incident Monday on CNN's "American Morning," TSA Administrator John Pistole said his understanding was the same as the account given by Baird.
The TSA is trying to strike a delicate balance, Pistole said - ensuring the safety of the traveling public while taking privacy concerns into account.