Port Authority spokesman Joseph Pentangelo said Justin Casquejo, 16, climbed through a foot-wide hole in the exterior wall at the site and was able to scale scaffolding around 1 World Trade Center made his way into the building and up to the top floor early Sunday, DNAinfo reported Thursday.
The New York Post said the teen may have donned a hard hat to trick an elevator operator into thinking he was working at the building.
Pentangelo said the teen spent at least an hour at the site before he was arrested around 6 a.m. Sunday. He was carrying a camera and a cellphone, which police confiscated.
Port Authority police said an "inattentive" security guard who allowed Casquejo to sneak past was fired.
"We take security and these type of infractions extremely seriously and will prosecute violators," said Joseph Dunne, the Port Authority's chief security officer. "We continue to reassess our security posture at the site and are constantly working to make this site as secure as possible."