The EC 135 model aircraft hit the ground in Aerzen, near Hamelin in northwest Germany, at around 1:45 pm. The reason for the crash is not yet known.
Firefighters rushed to the scene of the crash, which caused multiple blazes in a nearby forested area.
The impact site is around 30 kilometres from the Bundeswehr (German army) helicopter training centre in Bückeburg.
The pilot was killed and one person injured, a defence ministry spokesman told AFP.
As a result of the crash, a grain field burned first, a spokesman for the fire brigade said, and the flames were quickly extinguished.
“A military security area has been set up”, the Bundeswehr announced.
The EC 135 model is a light, twin-engined multi-purpose helicopter, which is mainly used for air rescue and surveillance tasks.
Another deadline crash
Just a week ago two Eurofighter jets crashed in northeastern Germany after colliding in mid-air, with one pilot killed while a second ejected to safety.
The military recovered both planes' black boxes and was investigating the cause of the crash, while some politicians called for a ban on training missions over populated areas.
Germany has in recent years suffered a string of problems with military equipment, with only fractions of its fleets of tanks, ships and aircraft combat-ready at any time.
The problems have persisted despite multiple increases in the defence ministry's budget, although spending remains below the NATO goal of two percent of GDP.