The crash happend at around 4:30am at a level crossing in Alt Duvenstedt, between Hamburg and Flensburg. The regional train, which was carrying 22 passengers, was derailed in the crash.
Eight people were injured, two of them seriously, police said. At first it was believed nearly all passengers had been hurt in the crash.
One of the injured was flown by helicopter to hospital in the port city of Kiel.
The accident happened when the cab of the articulated lorry, towing 70 tonnes of heavy equipment, became stranded at the level crossing. The driver jumped clear before the crash, police told news agency DPA.
Police said it was unclear why the truck became stuck at the crossing.
The impact badly damaged the front of the train, which was lifted off the tracks.
Rail travel between Flensburg and Hamburg is expected to be severely disrupted for most of Wednesday, police said, because of damage to overhead lines and the tracks.
"A special train from (national rail operator) Deutsche Bahn is coming to get the train that crashed back on the rails," a police spokesman told daily Bild.
"But the track where the accident happened will remain closed for hours because the rail bed has been affected."
The clean-up was continuing later on Wednesday morning as the pictures show.
Rescue workers inspect the scene on Wednesday. Photo: DPA
100 rescue workers at scene
A large contingent of rescue workers was initially deployed after the alarm was raised. Around 100 emergency service were on site to assist, authorities said.
Ambulances and a rescue helicopter transported those who'd been injured to clinics in the area.
People travelling in the region today have been warned they could expect disruption and delays.
Regional trains from Hamburg can only travel as far as Rendsburg, according to a railway spokeswoman. In the opposite direction, trains will end in Owschlag. The east-west connection between Husum and Kiel is also affected.
Investigations into the cause of the crash continue.
Last October, several people were injured in a similar accident between a regional train and an articulated lorry in Sipplingen, near Lake Constance, southern Germany.