Sixteen-year-old Justin Casquejo, of Weehawken, is charged with misdemeanor trespassing.
He allegedly broke in around 4 a.m. Sunday. He had no identification, but may have been dressed like a construction worker.
On Friday, Casquejo released an apology on his twitter feed. "I seriously apologize to anyone who may have been insulted or felt disrespected by my actions. It was not my intention to do so."
Police say he accessed 1 World Trade Center through a 1-foot-by-1-foot hole in the fence, and an elevator operator took him to 88th floor. He then climbed to 104th floor and walked past a sleeping guard. That guard has since been fired.
"Honestly I'm proud of him," friend Patrick Flores said. "I can honestly say, wow, this kid made a fool of the New York security."
The teen apparently had little trouble getting past security. He was stopped by another construction worker who spotted the red light on his GoPro camera as he attempted to leave the building, and police were called.
"We take security and these types of infractions extremely seriously and will prosecute violators," Port Authority Chief Joseph Dunne said. "We continue to reassess our security posture at the site and are constantly working to make this site as secure as possible."
"Obviously it's shocking and troubling and I don't know how it possibly could have happened," Mayor Bill de Blasio said.
Casquejo was detained by Port Authority police officers responding to a report of a unauthorized person on the site.
Casquejo was in possession of a camera and a cell phone and had apparently taken pictures from the top of the building, where he stayed for about two hours.
Port Authority officials said the breach and security at the site are all under investigation.
If Casquejo is convicted, he could face more than three months in jail.