The magnetic levitation Transrapid train, one of the world's fastest trains, was travelling at about 200km per hour in Emsland, near the city of Osnabrueck, at around 10am local time on Friday when it struck the wagon, police said.
The prosecutor's office in the city said that the collision had been caused by human error.
Most of those killed were passengers on the train, while reports say two more people standing on a train platform are also missing and feared dead, officials said.
Local television pictures showed rescue workers being hoisted up to the train on cranes to try to reach the accident site, while train seats, bags and clothes were scattered on the ground.
The crash occurred on a 32km circuit built as a testing facility for the train, which is propelled along at high speeds by a frictionless, electro-magnetic system known as Maglev.
A total of 29 people were on board, reports say.
Rescuers attempting to reach those trapped in the wreckage were being hampered by the height of the train, which rides on a track supported by concrete stilts about five metres above ground.
The train was developed by Transrapid International, a joint venture between German industrial firms Siemens AG and ThyssenKrupp.
Many of those travelling on the train were thought to be employees of the companies and their friends and relatives.
Wolfgang Tiefensee, the German transport minister, planned to cut short a visit to China, which uses a similar train between Shanghai airport and the city, to return home following news of the accident, German media reported.