No further details were immediately provided following the interception.
The Emek HaYarden region is located southwest of the Golan, near Syria.
Spillover fire from Syria's civil war has occasionally landed in the Israeli-controlled Golan. Israel is especially concerned about Iran's military presence in Syria.
In February, Israel intercepted what it said was an armed drone sent into its territory by Iran. A series of strikes in Syria that have killed Iranians have been attributed to Israel in recent months.
Iran is backing Syrian President Bashar al-Assad in the war, as is Russia. Today's incident came as Netanyahu travelled to Russia to meet President Vladimir Putin. Israel seized a large swathe of the Golan Heights from Syria in the 1967 Six-Day War and later annexed it, in a move never recognised by the international community.
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