Four additional injured passengers were taken to nearby Adventist Medical Center in Selma, while seven people were taken to Community Regional Medical Center in Fresno, officials said.
The train was on its way from Oakland to Bakersfield, according to Amtrak. It had four rail cars and a locomotive.
The truck driver suffered minor injuries, according to California Highway Patrol spokesman Jerry Pierce. Investigators will try to determine if the crash was caused by driver error, a malfunctioning crossing arm, or something else, the CHP said.
"This is a big, huge chaotic scene with lots of agencies involved," Pierce said.
Pierce said the other passengers were taken to an auditorium in Hanford, where they boarded another train and continued to their destinations or they were picked up by family members.
All train service through the area was halted after the crash.
Initially, Amtrak had expected to resume service through the area in time for the morning rush hour, but Amtrak spokesman Cliff Cole said late Monday that a bus bridge would carry passengers between Bakersfield and Hanford until at least 7:15 a.m.
"We will wait for further word from BNSF to see if we need to make further adjustments," Cole said.
BNSF Railway Co., which operates the tracks, expected to have the tracks open by 7 a.m., spokeswoman Lena Kent said.
Meanwhile, a second accident, this one around 4 p.m. Monday about 10 miles away involving a freight train and a tractor-trailer, left a truck driver with major injuries, the CHP said.