The train hit the truck at "up to 140 km/h", smashing it between 300 and 400 metres along the track and killing the drivers of the train and the truck, aged 35 and 30 respectively.
Firefighters had to use large amounts of extinguishing foam to put out a blaze that broke out in both vehicles, burning out both cabins.
Four other people were brought to hospital by helicopter to be treated for injuries but later released, while twelve people were slightly hurt.
The train had been carrying a total of around 40 passengers.
Bild reported that the heavy transport truck had been carrying a US military vehicle.
"We don't yet know why the transporter truck was standing on the level crossing," a spokesman for the Oberpfalz regional police headquarters said.
The stretch of track is completely closed until the recovery operation can be completed.