They described the find as one of the most significant since the Dead Sea Scrolls.
“For the first time in approximately 60 years, archaeological excavations have uncovered fragments of a biblical scroll,” Israel Antiquities Authority said.
Following a years-long dig in caves and cliffs in the desert east of Jerusalem, the authority said it had also discovered a cache of rare coins, a six-millennia-old skeleton of a child and basket it described as the oldest found in the world, dating back over 10,000 years.
The finds are the result of survey of about 80 kilometres of cliffs in an arid area spanning southern Israel and the occupied West Bank.
Using drones, mountain climbing gear and rappelling equipment, Israeli archaeologists searched caves they said were used by Jews rebelling against the Romans during the failed second-century Bar Kochba revolt.
The fragments of the scroll include passages written in Greek from the Book of the Twelve Minor Prophets, part of the Hebrew Bible, the IAA said.
One fragment from the book of Zechariah reads: “These are the things you are to do: Speak the truth to one another, render true and perfect justice in your gates.”
Although most of the text is in Greek, the name of God appears in ancient Hebrew script, the IAA said.
Israeli archaeological excavations in occupied Palestinian territory are divisive, but the Palestinian Ministry of Tourism and Antiquities did not respond to requests for comment.
The IAA co-operated on the project with the military branch responsible for civil affairs in the Palestinian territories, Cogat.
Spokeswoman Yoli Shwartz said it was one of the most significant discoveries of a Biblical text since the Dead Sea Scrolls.
What are the Dead Sea Scrolls?
The Dead Sea Scrolls include the remains of about 900 manuscripts found between 1947 and the mid-1960s in and around the Qumran caves, above the Dead Sea in the West Bank. They are some of the earliest biblical texts discovered.
IAA director Israel Hasson said the survey had begun in response to looters who slipped into the caves.
He called the finds “a wake-up call” for devoting more resources to continue the project, which has only surveyed about half of all the cliffs in the desert.
“We must ensure that we recover all the data that has not yet been discovered in the caves, before the robbers do,” Mr Hasson said.