Parcels containing cannabis and so-called legal highs were removed at HMP Altcourse in Liverpool.
The contraband had become lodged on the 60ft (18m) roof after attempts were made to throw it over the prison walls.
A prison spokesman said the crane is now being used as a deterrent, "a bit like visible police street patrols".
Dave Thompson, director of the privately-run Category B jail, said: "These items were thrown over the prison walls by criminals on the outside.
"We are committed to preventing drugs coming into our prison and we are encouraged that at the same time as our seizures of banned substances have increased, the numbers of prisoners testing positive for them has come down.
"Altcourse's latest independent inspection report by government monitors praised our drug intelligence work, which they said led to effective drug searches in the prison."
Government figures confirmed that 290 mobile telephones and SIM cards were seized in Altcourse in 2013 - the second highest number in England and Wales.
Prison staff had to use a "cherry picker" crane to remove packages of drugs and mobile phones which had become trapped on the roof.