It will be the latest "security fence" built by Israel, including one separating it from the West Bank and another in the Golan Heights near Syria.
Prime Minister Benjamin Netanyahu said when it was approved in June that the new fence was a continuation of a 240-kilometre (150-mile) barrier built along the Egyptian border which "blocked the entry of illegal migrants into Israel and the various terrorist movements".
"This barrier is intended to protect Israeli citizens against any security threat coming from Jordan," Arielle Heffez, a spokesman for the ministry, told AFP on Wednesday.
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In 2013, Israel erected a 240-kilometre electronic fence along its southern border with Egypt.
The Jordanian fence will be "based on the models erected along the Egyptian border and the Golan Heights," the defence ministry said.
It will include "roads, observation towers, operations rooms and other advanced means."
The barrier will be 30 kilometres (19 miles) long between the resort city of Eilat and the site of the Sands of Samar and will cost 300 million shekels ($75 million, 70 million euros), according to the statement.