The train struck the pedestrian just south of Union Station. Officials believe the pedestrian was a transient.
Police Officer Sara Faden says the call was received at 6:18 a.m. Wednesday but there are no details.
Thirty people were aboard the train, including passengers and crew members, and no one was hurt, an Amtrak spokesperson said.
Metrolink commuter trains are delayed because of the investigation.
Metrolink says in Twitter postings that Orange County lines 601, 603, 605, 683 and Riverside County lines 701 and 703 are affected and alternate travel arrangements are necessary.
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