The agreement also allows an unlimited number of charter flights to the smaller Ramon Airport outside Israel's southern resort city of Eilat, Xinhua news agency reported on Sunday.
Additionally, some 10 cargo flights could be operated per week under the deal.
The flights in the new route are expected to begin in a few weeks, according to the ministry.
The agreement comes after a US-brokered normalization deal between the UAE and Israel was signed at the White House on September 15.
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