A delegation from a Council of Europe committee visited the jail in Riddrie, Glasgow.
They raised concerns about excessive force used by staff, overcrowding, remand prisoners spending up to 22 hours a day in cells and new inmates being confined to "cupboard-like cubicles" - known among prisoners as "dog boxes" - during the admission process.
In a report, just published by the Committee for the Prevention of Torture and Inhuman or Degrading Treatment or Punishment (CPT), they said two prisoners reported being "punched" by staff.
One inmate told the group that he was "punched to the right side of the head" for not obeying an order to end a phone call.
Another, who was already said to have been brought under control using "control and restraint" methods, was also allegedly punched.
In their report, the CPT said prison officers should be reminded that "no more force than is strictly necessary should be used to control prisoners".
They added: "There can be no justification for striking a prisoner after he or she has been brought under control or for physically assaulting a prisoner who refuses to obey an order."
The body also hit out at the small cells in which prisoners are initially placed and the lack of activities for remand or untried prisoners.
They said: "The CPT is critical of the 63 cupboard-like cubicles in which prisoners are placed during the admission process to Barlinnie Prison.
It also criticised the finding that remand prisoners "often spend up to 22 hours a day confined to their cells and recommends that action be taken to develop the number of purposeful activities on offer".
The report says that generally cells were "in a satisfactory state of repair and cleanliness".
Occupancy levels in the prison, which was operating at 120% above its design capacity of 1021 places, have also been reduced, it was reported. But around 400 prisoners continue to be "cramped" together and held two to a cell, say the CPT.
The body said the death of an inmate on June 17 2012, who was known to have mental health issues and was a self-harming risk "raises questions as to the effective-ness of the monitoring system" for such patients.
The delegation also visited Greenock Prison, Kilmar-nock Prison, and all-female Cornton Vale, Stirlingshire. All visits took place in 2012 but the report was published in Strasbourg this week.
It said serious incidents of "inter-prisoner violence" were generally low and the prisons had anti-bullying policies.
But the group said inmates at Kilmarnock Prison stated "stronger groups of prison-ers would come into their cells, push, insult and intimidate them, and that staff did little to prevent such behaviour".
They also described a hospital cell in the jail, where a cancer patient was being treated, as "rather dirty".
The CPT is given unlimited access to places of detention across Europe to assess how people deprived of their liberty are treated.
The body has the right to move inside them without restriction and interview those detained in private.
A spokeswoman for the Scottish Prison Service (SPS) said: "We have noted the CPT's comments concerning the admission procedure at HMP Barlinnie.
"The safety and welfare of those in our custody is para-mount, and we are comm-itted to the taking forward either the redevelopment or replacement of HMP Bar-linnie as part of our estates development strategy.
"In the shorter term, we will take steps to improve facilities within the reception area.
"Our staff aim to reduce a negative impact on prisoners by offering constant support, access to facilities and refreshments during the admissions process."