Amtrak's Downeaster trains normally run from Boston to Brunswick, Maine, which stops in Portland and Dover, N.H.
The agency also said later Friday that its trains from Washington, D.C. were stopping in New York City. The trains usually continue on to Boston.
Amtrak tweeted Friday as the service interruption stretched to four hours that "a decision about restoration of #Amtrak service into Boston will be made when local authorities inform us operations can resume."
Service on Boston's "T" subway system has also been suspended, and the Federal Aviation Administration has also restricted the air space over a three-mile wide area of Boston because of the manhunt.
-This story was updated with new information at 1:49 p.m.