Tim Allen, a Londoner headed from New York to Boston, said he endured similar false alarms recently in London. "This is the second time this has happened in two and a half weeks to me," he said.
The incident was over as quickly as it began. One minute, camouflage-clad soldiers were shouting, "Penn Station is closed indefinitely," and the next minute they got the all-clear and started letting people back into the station.
The service disruption affected Amtrak, the Long Island Rail Road, New Jersey Transit and the Seventh and Eighth Avenue subway lines.
Also Sunday, a double-decker Gray Line tourist bus was evacuated in midtown Manhattan after a bus company supervisor told police that five male passengers with backpacks and "stuffed" pockets had raised her suspicions. Police handcuffed five men and searched about 60 passengers before determining there was no threat.
Authorities in New Jersey began searching the bags of bus and train riders on Monday, although acting Gov. Richard J. Codey said last week there is no specific threat about attacks against the state.
About 800,000 passenger trips are recorded every weekday on NJ Transit, with about a half-million on buses, 230,000 on trains, and the rest on light rail.
Travelers who refused the searches would not allowed to ride.
The American Civil Liberties Union said the inspections violate protections against unreasonable searches. Edward Barocas, legal director of the group's New Jersey chapter, said it was too early to determine what, if any, action the group would take.
Terrorism expert Jessica Stern told CBS News' The Early Show that "there are measures that can be taken" to protect ourselves from attacks, but she's not sure searching bags is the best idea.
"I must say that observing what's going on in New York now, I do wonder whether it would behoove them to try what the state police are doing at Logan Airport [n Boston], which is trying to determine behavioral profiling, indicators, rather than looking in people's bags."