At about 2:30 p.m., a Union Pacific freight train hit a person on the tracks near Main Street, south of Amador Valley High School, authorities said.
The train was headed southbound and was not near a crossing when the pedestrian was hit, Union Pacific spokesman Aaron Hunt said.
The accident blocked a set of tracks used by both Union Pacific and ACE, which led to 60-minute delays for commuter train No. 4, ACE spokesman Thomas Reeves said.
The agency planned to set up a bus bridge between stations, he said.
The site should be cleared by about 5:15 p.m., according to Reeves, and the next two commuter trains are not expected to experience delays.