The Petra state news agency said the ministry will handle non-military logistics, administration, investments, and development, allowing the army to "devote itself to its military and professional duties."
Jordan's prime minister has traditionally held the post of defense minister, but no such ministry has existed since the 1950s.
Jordan has been spared the violence engulfing its neighbours, but the military has had to redouble efforts to guard the borders as well as manage the influx of more than 600,000 Syrian refugees, many of whom live in the massive Zaatari camp.
In April, Jordanian warplanes struck a convoy of vehicles as they were trying to enter Jordan from Syria. The Jordanian military said the aircraft destroyed the vehicles after firing warning shots. Last month the Jordanian military said the air force had shot down an "aerial target" near the northern border with Syria. Witnesses described the object as a drone.
The kingdom has quietly supported Syria's rebels since the start of the uprising against President Bashar Assad in 2011, and ordered Syria's ambassador out in May after accusing him of making "offensive" statements about Jordan.