During an inspection in March, the prison was found to have improved slightly but is still not meeting the internationally recognised standards of a 'healthy prison', the report said.
It was the first since Maghaberry was deemed a failing prison in a heavily critical assessment by inspectors in 2009.
"This inspection found signs of real improvement which are welcome, but the prison still has a long way to go. It does not yet provide a sufficient level of safety and respectful treatment with too many prisoners having insufficient purposeful activity during their time there," explained Brendan McGuigan, Chief Inspector of Criminal Justice in Northern Ireland.
Support for vulnerable prisoners were found to be improving, with the multi-disciplinary team in the Donard Day Centre praised for providing excellent care.
But concerns were raised about prescription medicine being diverted from prisoners and poor drug treatment processes.
"Clearly the bullying and intimidation of prisoners still goes on and worryingly, sometimes prisoners who are on prescription medication are bullied to hand it over to other prisoners, and it creates an opportunity for a black market," Mr McGuigan told U105.
"The Prison Service are looking to see that prisoners only receive their daily dose, so it's not available for other prisoners to intimidate and bully them."
Inspectors also noted that there was no effective monitoring of violent incidents to identify when or where they were likely to occur or how they could be prevented.
The inspection team found that despite high staffing levels, association and exercise areas were not adequately supervised and concerns remain that Maghaberry does not provide a sufficiently safe environment for prisoners held there.
Brendan McGuigan, NI Criminal Justice Chief Inspector
Nick Hardwick, Her Majesty's Chief Inspector of Prisons in England and Wales called for a more strategic approach to learning and skills to be adopted within Maghaberry Prison.
"There has been positive investment in the prison's new Learning and Skills Centre but the provision available at the time of the inspection, was failing to meet the needs of the prison population," he said.
Mr Hardwick said there were insufficient activities to occupy prisoners with around half of the prison population unemployed.
This meant too many prisoners were being locked behind their doors for up to 20 hours per day.
The report states that in relation to its resettlement activity, outcomes for prisoners were assessed as being 'reasonably good.'
The report said that resettlement was the most positive aspect of Maghaberry Prison, with good attempts made to address the behaviour of both short and long-term prisoners despite high numbers and the complex range of prisoners held there.
Maghaberry's own statistics have confirmed that in terms of equality there were still unequal outcomes for Catholic prisoners in several important areas.
Brendan McGuigan, NI Criminal Justice Chief Inspector
Among other findings, the inspection report said there had been no progress to address the long-standing issue of disparity in treatment between Catholic and Protestant prisoners, with Catholics not faring as well.
The unequal outcomes primarily related to the granting of benefits or application of sanctions where staff had a measure of discretion.
"Yet this sensitive issue was not being addressed and we have recommended the Northern Ireland Prison Service to take action to deliver equality of outcomes for all prisoners," he added.
Issues were also raised about the structure of health care within the prison, the report notes organisational and staffing problems having "an adverse impact on clinical outcomes". Healthcare partnership arrangements were also found not to be working effectively.
The Chief Inspector said: "The progress made to date needs to be increased and Inspectors would encourage the Northern Ireland Prison Service to embed these improvements in the culture and processes at Maghaberry Prison so that the progress that has been made is built on further."
NI Prison Service Director General Sue McAllister said that of the six main recommendations and nearly 90 others, all but four points had been accepted by the Prison Service.
"While there is still much room for improvement, progress has been made in three of the four 'healthy prison' tests, with the fourth remaining unchanged," she said.
The Director General praised the efforts of staff in helping to bring about improvements for the prison population and said that some of the issues raised by the Inspectorate were being addressed as part of the wider Prison Estate Strategy.
The Governor of Maghaberry, with my total support, is committed to delivering on the changes recommended by the Inspectorate and the Action Plan, addressing each of the recommendations will serve as an important driver for change and is in keeping with the wider Prison Service Strategic Efficiency and Effectiveness Programme.
Sue McAllister, NI Prison Service Director General
She said: "The Inspectorate found that some elements of physical security were 'overbearing'. In an interim statement to the Assembly last month the Justice Minister said that Maghaberry would be reconfigured into three 'mini prisons,' which will allow prisoners to be accommodated in areas of the prison where security measures will be commensurate with their level of risk. This will, as a consequence, allow for enhanced regime delivery.
"Outcomes for prisoners on issues of resettlement have been lauded by the Inspectorate and the positive work being undertaken in this area is to be commended. They noted however that the closure of the Prisoner Assessment Unit had a detrimental effect on some long-term prisoners.
"The recent announcement by the Minister that the Prisoner Assessment Unit will be redeveloped is therefore to be welcomed and I will work with colleagues to ensure that his can happen as soon as possible and in a manner which will command support from all sides."