Several people were hurt in the collision, which happened around 2:05 p.m. at NE Maynard Road and East Chatham Street.
Cary Police said a construction trailer detached from a truck that was crossing the tracks and was resting on the tracks when the train came through.
Authorities said that at least six people were injured. Four people were taken to a hospital, EMS crews told ABC11.
All injuries appeared to be minor, EMS said.
Amtrak told ABC11 that train 72 was traveling from Charlotte to Raleigh with 46 passengers onboard.
"I was in the train, looking out the window, there was kind of a large jolt," said Caleb Walker, who was a passenger in the front car of the train. "I saw everyone looking around, and I looked out the window, and there was like a cloud of concrete dust that floated by."
The train traveled about a quarter of a mile after the collision before coming to a stop.
Passengers scrambled to figure out what was happening.
"Now I really was, I was like, what's happening? Because I thought the trains were shifting like the tracks," said one passenger, who did not want to be identified. "But then everyone's like hooting and hollering, like insane to her. And I look and I, that's when I see the thing flip ... So I'm like, oh, like, we just hit something."
Passengers were OK, but some were left figuring out their travel plans.
"It started raining as soon as they let us off. So we all just kind of flocked to the Bojangles, and it was just full of people with luggage for a while," Walker said.
Cary Police units are working with CSX Transportation, Amtrak, NCDOT, and Cary Fire to clear scattered debris. NE Maynard Road is closed between Chapel Hill Road and E. Chatham Street and did not reopen until late Wednesday night -- more than seven hours after the crash.
CSX, which runs the track, said it was able to get it repaired.
"These incidents can affect everyone involved - those who are injured or die and their families, our train crews, and our passengers," Amtrak said in a statement. "They also serve as critical reminders about the importance of obeying the law and of exercising extreme caution around railroad tracks and grade crossings."
The train was able to resume its route late Wednesday afternoon.
Nolan Williamson, who has followed trains around the Triangle as a hobby for 10 years, said more and more, he sees cars in dangerous situations too often, before the lights come on and the arms go down.
This is pretty bad. I've noticed a lot. Yeah, there's, it's all with the drivers and, you know, them not being careful at the crossings and, you know, stopping on the tracks and all that," Williamson said. "It's they have posted signage everywhere. It says don't stop on the tracks. And, you know, people you know like to cross the tracks at, you know, on designated crossings, just like across the tracks."
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