The man in custody is injured, police said in a tweet.
The station is one of the busiest commuter hubs during rush hour.
The A, C and E subway lines were evacuated, NYPD Sgt. Brendan Ryan said. The subway entrance on Eighth Avenue and the bus terminal are closed, the Port Authority said in a tweet, adding that there was still police activity in the area.
There are no deaths reported, a federal law enforcement source said.
“Could have been a lot worse,” the source told CNN.
Preliminary information, according to two law enforcement sources, one local and one federal, indicates a pipe bomb may have unintentionally exploded.
A man wearing a homemade device attempted to detonate it, and it either malfunctioned or did not go off the way it was supposed to, according to one NYPD source.
Francisco Ramirez said he heard two explosions as he was exiting a bus about 7:45 a.m. ET. He heard both blasts distinctly even though he was wearing headphones.
“From what I saw it sounded like it came from the subway, but I’m just guessing,” he said. “It was two distinct explosions seconds from each other. As I was making my way toward the outside, I kept getting shoved by cops and there were cops at every entrance blocking and there was police and SWAT everywhere.
“It was scary. It was just a lot of chaos but I didn’t see any injuries.”
Marlyn Yu Sherlock was at a retail store on the main floor of the terminal when people began flooding out of the subway entrance, “screaming, running in panic,” she said.
“The PA system was still blaring Christmas carols,” Sherlock said. “It took about four minutes before men in black cop uniforms started shooing people out of Port Authority. As I walked further away from the building, I kept asking the heavily armed cops what it was. They said ‘suspicious package.'”