A Denver media outlet is reporting that the FBI is now calling the Amtrak Threat incident a "complete misunderstanding."
The man has apparently been released from FBI custody and taken to Denver International Airport to board a flight.
Officials say it all started just before 10 o'clock Sunday night after a passenger threatened the crew and others on board claiming he had a gun and a bomb. The train holding more than 140 people was then evacuated as a precaution.
A spokeswoman for Amtrak said no injuries were reported.
The spokeswoman, Karina Romero, said the train's crew alerted authorities after the passenger made claims he had a weapon and bomb.
Police met the train about 22 miles west of Denver, detained the man and did a sweep of the passenger and baggage cars.
Officials said the man was carrying a knife and a bomb-sniffing dog focused on his bag.
Passengers were evacuated and transported by bus to Denver.
The California Zephyr train travels each day from Emeryville, California to Chicago.