It took several hours to sweep the empty Newark concourse Sunday night. Passengers were allowed to go back through security just before midnight.
"We had to take action that unfortunately inconvenienced a hell of a lot of people," the TSA's Davis said.
Continental says more than 100 flights were impacted, and though the operation is "looking good" today, there are still some international flights that were behind schedule Monday afternoon.
"We're going to look at the timeline to see how we could have done better," Davis said.
These kinds of episodes happen on occasion, the TSA says. In the week that began Dec. 14, the agency says there were 37 incidents at airports across the country that involved a checkpoint closure, terminal evacuation or a sterile area breach.
Sunday's breach at Newark comes as the TSA implements new security procedures or passengers flying into the US from countries tied to terrorism, in the wake of the attempted Christmas day bombing of a plane headed to Detroit.
Passengers on flights arriving from Paris and Mumbai told ABC News they were frisked at their departure gates, and every piece of their carry-on luggage was searched.
"You had to take off your jacket, you had to take off your purse, they went through your purse and did the whole body thing," one passenger said.