The massacre also includes what could be one of the earliest records of torture.
Archaeologists dug up 26 bodies in a mass grave and said the horror of their deaths marked them out.
The remains were first dug up in 2006 in Schoneck-Kilianstadten, about 15 kilometres outside Frankfurt, and now researchers have closely examined the bones.
The legs of the victims seem to have been broken - either just before or just after death.
"Many have injuries, skull fractures caused by typical weapons from the time," said Christian Meyer, who was a PhD student at the University of Mainz when he conducted the research.
Also Read
"We can say these people were violently killed, at close quarters. The legs are a new thing, though. This has not been encountered before. The lower leg bones, the tibia and fibula, appear to have been smashed systematically," Meyer said.
"Basic human common sense tells you this has to be either torture or mutilation," Meyer said.
There were no young women among the dead, researchers found.
"This pattern is repeated all over the world at different times. Basically you kill everyone. If you spare someone, it is usually women of reproductive age - you take them with you," Meyer said.
"These three places prove that 7,000 years ago there was already collective violence on a large scale," Meyer said.
The research is published in Proceedings of the National Academy of Sciences.