The corpses of ten people were found outside Strasbourg in one of 300 ancient "silos" used to store grain and other food, a team from France's National Institute for Preventive Archaeological Research (Inrap) told reporters.
The Neolithic group appeared to have died violent deaths, with multiple injuries to their legs, hands and skulls.
The way in which the bodies were piled on top of each other suggested they had been killed together and dumped in the silo.
"They were very brutally executed and received violent blows, almost certainly from a stone axe," said Philippe Lefranc, an Inrap specialist on the period.
The skeletons of five adults and one adolescent were found, as well as four arms from different individuals.
The arms were likely "war trophies" like those found at a nearby burial site of Bergheim in 2012, said Lefranc.
He said the mutilations indicated a society of "furious ritualised warriors", while the silos were stored within a defence wall that pointed towards "a troubled time, a period of insecurity".
It is hoped that genetic testing on the bones will reveal more information about the killings, but Lefranc said one theory was that a local tribe had clashed with a new group arriving from the area around modern-day Paris.
"It appears that a warrior raid by people from the Parisian basin went wrong for the assailants, and the Alsatians of the era massacred them," he said.
However, in the long run, it was the "Parisians" who had the last laugh.
The local tribe appear to have been supplanted by the newcomers around 4,200 BC, as demonstrated by new funeral rites, pottery and hamlets.