The discovery once again shows similarities between humans and our ancient cousins, they said.
The findings indicate Neanderthals butchered animals, made tools and gathered around the fire in different parts of their shelters, they said.
"There has been this idea that Neanderthals did not have an organized use of space, something that has always been attributed to humans," anthropologist Julien Riel-Salvatore, at the University of Colorado Denver and lead author of the study, said.
"But we found that Neanderthals did not just throw their stuff everywhere but in fact were organized and purposeful when it came to domestic space."
The evidence comes from excavations at a collapsed rock shelter in northwest Italy where both Neanderthals and, later, early humans lived for thousands of years, the researchers said.
Neanderthals divided the cave into different areas for different activities, they said. The top level was used as a task site, likely a hunting stand, where they could kill and prepare game. The middle level was a long-term base camp and the bottom level was a shorter-term residential base camp.
"This is ongoing work, but the big picture in this study is that we have one more example that Neanderthals used some kind of logic for organizing their living sites," Riel-Salvatore said.
"If we are going to identify modern human behavior on the basis of organized spatial patterns, then you have to extend it to Neanderthals as well."