The well, discovered in the Jezreel Valley in the northern Galilee region, contained a variety of artefacts, as well as the remains of a woman approximately 19 years old, and an older man, the IAA said.
Archaeologists said it was unclear how the pair came to be in the well, but hailed the discovery of the ancient water source.
"Wells from this period are unique finds in the archaeology of Israel and probably also in the prehistoric world in general," said Omri Barzilai, head of the authority's prehistory branch.
Remains of skull found in well (Photo: Clara Amit, courtesy of Israel Antiquities Authority)
He said one other well of a similar age had already been discovered in Israel.
"The two oldest wells in the world were previously exposed in Cyprus and they indicated the beginning of the domestication phenomenon: it seems that ancient man tried to devise ways of protecting his drinking water from potential contamination by the animals he raised," he said.
"The exposure of these wells makes an important contribution to the study of man's culture and economy in a period when pottery vessels and metallic objects had still not yet been invented," he added.
IAA worker inside the well (Photo: Yotam Tepper, courtesy of Israel Antiquities Authority)
Yotam Tepper, IAA excavation director, said numerous artefacts were recovered from inside the well, including sickle blades and arrow heads.
"The impressive well that was revealed was connected to an ancient farming settlement," he said.
Tepper added that the well demonstrated "the impressive quarrying ability of the site's ancient inhabitants and the extensive knowledge they possessed regarding the local hydrology and geology, which enabled them to quarry the limestone bedrock down to the level of the water table."