An Amtrak spokesperson said a passenger found a suspicious note in a restroom. He did not elaborate on what was in the note.
Police say the search was a "routine sweep'' and the train was allowed to continue.
These kinds of searches, asking passengers for identification, will become routine leading up to next month's GOP convention in New York.
Law enforcement officials in Boston are also getting ready to protect that area during the democratic national convention, which begins next week.
Agencies involved in protecting the Convention Center have a machine to help check out suspicious packages without having to risk the life of a police officer. It operates by remote control.
Police will also have a large amount of riot gear and non-lethal weapons available if protestors get out of hand.
The Associated Press and CNN contributed to this report.