Nothing dangerous was found and passengers endured an 11-hour delay, arriving in Whitefish just before 7:30 a.m. Tuesday.
Amtrak spokesman Marc Magliari said a passenger was removed from the train in Browning shortly before 8:30 p.m. Monday. While being interviewed by local authorities, the man "somehow threatened the safety of the train."
The train was stopped between Browning and East Glacier and its 150 passengers were taken to a middle school in Browning. Magliari says a K-9 unit helped search the train.
Officials did not release the man's name or say where he boarded the train, which travels from Chicago across northern North Dakota and Montana to Seattle and Portland, Ore.
The search of the passenger train held up at least 50 freight trains, said BNSF Railway spokesman Gus Melonas. BNSF property was also searched in light of what Melonas called a bomb scare. Train traffic was shut down for about seven hours, Melonas said, and other recent weather delays have led some freight traffic to be delayed more than 24 hours.
The search of the train took more than eight hours. The remainder of the delay occurred when Amtrak had to bring in a new crew because the crew on the train had reached the limit on the number of hours they could work, Magliari said Tuesday.
The trip from Browning to Whitefish usually takes about an hour by train.
Glacier County officials said the man who was removed from the train was being held in the Glacier County jail in Cut Bank.
FBI spokeswoman Debbie Dujanovic Bertram said investigators will present a case to the U.S. attorney's office for possible charges.
The evacuated passengers were set up with sleeping bags and air mattresses at the middle school.
"We appreciate the hospitality of the Blackfoot Nation," Magliari said.