Written in Hebrew more than 2,000 years ago, it is one of 870 scrolls discovered between 1947 and 1956 in the Qumran caves above the Dead Sea.
"It's not usually exhibited... because it's very sensitive and fragile," a museum official told AFP on condition of anonymity, adding that it was being displayed in a climate-controlled glass case.
When not on show, the scrolls are kept in a dark, climate-controlled storeroom in conditions similar to those in the Qumran caves, where the humidity, temperature and darkness preserved them for two millennia.
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The Ten Commandments scroll is part of "A Brief History of Humankind", a unique exhibition on human development drawn from the museum's collections that includes the original handwritten manuscript of Albert Einstein's theory of relativity.
The scroll, which measures 18 by 2.7 inches (46 x 8 cm), has been displayed in the past in the United States.
The museum said that owing to its fragility it would be on display for "up to four weeks, after which an exact facsimile will be on display."
The Brief History of Humankind exhibition, part of the museum's 50th anniversary celebrations, runs until January 2, 2016.