The family were pulled up after a juice bag was found in Vendela's bag. She'd left it there by accident as she processed through security at Raleigh-Durham International Airport.
Payne says it was an uncomfortable experience but he tried to remain calm in an effort not to cause a scene.
"I just kept it as calm, cool, compliant as possible, and she followed suit," Payne told San Diego Union Tribune. "Deep down I was absolutely fuming, but I knew letting emotions out was only going to worsen the situation for everybody."
Payne filmed the incident and posted the footage to YouTube.
He said his daughter had never been through an extra screening process but kept calm in an effort not to "throw a tantrum like a one-year-old".
Vendela said she understood the reason behind the process but felt the TSA agent went too far.
"I know it's to keep everybody on the plane safe, but she kept patting me down,' Vendela told NBC. 'Pat down, pat down. It was like, over and over."
According to the TSA's website, screenings are performed to identify threats and prohibited items "which may be concealed under clothing".
It notes during pat-downs, sufficient pressure must be applied to ensure detection, but the process has been modified for children under 12 years old.
It also says the agents will discuss the best way to relieve any concerns during the screening of a child about the best way to relieve any concerns during the screening.
Payne said the actions looked like what would be applied to an adult, not a child and told NBC it seemed the "pat-down" was just a go-to for the agent.
"My goal was just to clear security as quickly as possible so we could make our flight even though I knew that in my mind they shouldn't be doing what they were doing," Payne said.
"I didn't want to make an issue of it there or then because it wasn't the time or place and I didn't want to further traumatize my daughter."
TSA spokesman Nico Melendez gave the Union Tribune a statement about the incident.
"Since pat-down screening is conducted to determine whether prohibited items are concealed under clothing, sufficient pressure must be applied in order to ensure detection," the statement said.
The security check delayed Payne's family trip for about an hour, and they only made their flight because it was delayed.
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- nzherald.co.nz