The Direct Rail Services (DRS) train, which was on its way to the Sizewell A nuclear power plant on Monday, hit the Ford Focus at Knodishall in Suffolk.
A British Transport Police spokesman said it did not derail, no-one was hurt and there was no danger to the public.
He said the train was checked and continued on its journey shortly after.
"The train was travelling at between 15mph and 20mph when it struck a blue Ford Focus, which had encroached on to the crossing in Clay Mills Road," added the spokesman.
"This was a minor low-speed collision on a level crossing.
"There were no injuries and no danger of contamination."
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