As punishment for escaping and for the robberies committed while on the run, Johns received five years' hard labour on top of his remaining sentence. Extraordinary measures were taken to ensure that Johns did not escape again. He was sent to Fremantle Prison, and kept in the yard with his neck chained to the iron bar of a window, while a special "escape-proof" cell was made for him. The stone-walled cell was lined with jarrah sleepers and over one thousand nails, and was almost air-proof and light-proof. Johns was kept in the cell on a bread and water diet, with only one to two hours of exercise a day. In early 1867, due to his diminishing health, Johns was set to work breaking stone in the open air but, rather than permit him to leave the prison, the acting comptroller-general ordered that the stone be brought in and dumped in a corner of the prison yard, where Johns worked under the constant supervision of a warder. Governor John Hampton was so confident of the arrangements, he was heard to say to Johns: "If you get out again, I'll forgive you". However, the rock broken by Johns was not removed regularly, and eventually a pile grew up until it obscured the guard's view of him below the waist. Partially hidden behind the pile of rocks, he occasionally swung his sledgehammer at the limestone wall of the prison.