The scanners were previously introduced in the 10 Prisons Project to crack down on violence and drug use at HMP Leeds.
Other prisons included in the project included Hull, Humber, Isis, Lindholme, Moorland, Wealstun, Nottingham, Ranby, and Wormwood Scrubs.
Steve Robson, the governor of HMP Leeds, said the addition of a scanner had been a "real game changer".
He said: "In the year it has been in operation, it has found over 300 items of contraband, with prisoners finding drugs harder to come by at Leeds."
The scanners will now be introduced at 16 of the country's "most challenging" jails following the success at jails across Yorkshire.
Birmingham, Liverpool and Winchester will be the latest three prisons to receive the technology before it is rolled out to Exeter, Durham, Preston, Hewell, Lincoln, Bedford, Norwich, Chelmsford, Elmley, Pentonville, Wandsworth, Bristol and Cardiff later in the year.
Around £28 million, out of a £100 million fund to boost security in prisons, will be used to pay for all the scanners which are eventually hoped to be installed in the majority of closed adult male jails.
The contract for providing them has been awarded to company Adani Limited.
Aidan Shilson-Thomas, from the think tank Reform, said the plan will "get the ball rolling on stabilising the system" but said the MoJ "must ensure that the prisons have the resources to staff these new measures", adding: "The next step must be to help prisoners struggling with addiction, which in turn will reduce prison violence and re-offending."
Prisons Minister Lucy Frazer said: "New technology is a vital part of our efforts to stop those determined to wreak havoc in our jails.
"These scanners will help to stem the flow of contraband into jails and allow officers to focus on rehabilitation."