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.

Smith was named captain of the Red Rose for the 2015 season, but only skippered the team in one game after being told he needed back surgery.
The injury kept him out for 13 months but he came back to feature in the final months of last season, only for back problems to return.
"It's very sad and a tough decision to come to," he told BBC Radio Lancashire.
"Following some medical advice from the specialist and thinking about the long term future it has come because of injury.
"The highs of lows of the past two years from captain to not playing, to surgery, to back playing, to retiring but ultimately it has taken its toll. My long-term health has taken priority."
The club have announced that Smith will stay at Old Trafford to assist academy director Gary Yates in helping bring young players through their system.
BBC Radio Lancashire cricket reporter Scott Read:
"Tom Smith can look back on his career with a great deal of pride for both his performances on the field Lancashire and for the courage he showed off it.
"He fought hard to return from injury last season, an injury which robbed him of the captaincy in 2015.
"A genuine all-rounder, who consistency with the bowl and skill with the bat saw him named the club's player of the year after a stellar 2014.
"He'll be admired and respected at Old Trafford in equal measure both as a player and a person."

Daniel Braxton was driving through Towyn, Conwy county, with his 18-year-old daughter at 07:15 BST on Tuesday.
She thought she saw a dead baby in the bus stop near the Magpie and Stump pub and screamed at her father to drive back to check, which he did.
Mr Braxton, 35, said he saw the lifeless naked baby on the ground, with her umbilical cord still attached.
"We blocked the road off and rang the emergency services," he told BBC Radio Wales.
"I had a dressing gown in the car and ran to grab that, wrapped the baby up, gave her some good hard rubs on the chest and the head.
"She took one big gulp of breath and opened her beautiful little eyes."
Mr Braxton, who is originally from Birmingham and living in nearby Pensarn, said they guessed that the baby was less than one hour old.
"To be honest, I think the fatherly instinct and the adrenaline kicked in because my daughter was hysterical and my partner was hysterical," he added.
"So it was just a case of as soon as I saw her lying there, her naked little body just left on cold concrete, I knew something had to be done."
Mr Braxton said police have told him that the baby has "stabilised and is on her way to a full recovery".
Police are concerned about the welfare of the baby's mother and have urged her to come forward.
Helen Douglas, of North Wales Police, said: "We are concerned about the health of the mother of the baby girl and are appealing for her to come forward.
"Alternatively, if anyone knows who the mother is or can provide any information which may assist in identifying her please contact North Wales Police.
"We want to ensure that the mother is provided with the medical support she needs."
Prison staff had to use a "cherry picker" crane to remove packages of drugs and mobile phones which had become trapped on the roof.
[NEXT_CONCEPT]
Lancashire all-rounder Tom Smith has announced his retirement at the age of 31 after a series of injury problems.
[NEXT_CONCEPT]
A man has described how he managed to revive a lifeless newborn baby which was found in a bus shelter.