The inspectors, who visited the prison in April, found at-risk prisoners were being held in dry cells when the ISU's "safer cells" were full.
However, Boshier said the inspection this year showed there had been significant improvement since a previous inspection three years ago.
The prison was now cleaner, tidier and in better repair than it was three years ago, and general living conditions for most prisoners had improved, he said.
He was also pleased to find two-thirds of 18 recommendations he made in 2016 were being actioned, including that cells were kept in a clean and decent state of repair.
But there was still significant room for improvement in multiple areas and beyond the use of dry cells he raised concerns about:
• An absence of therapeutic activities, and intervention and support for prisoners experiencing mental distress;
• Extended periods of isolation for prisoners in the ISU (up to 23 hours a day);
• The ISU being used as the default management unit following use of force, which undermined the intended purpose of the environment; and
• The weekly staff rotation in the ISU, resulting in some staff not building the necessary skills and experience to work with prisoners experiencing mental distress.
Boshier welcomed the introduction of two new cultural and arts programmes for a small group of prisoners awaiting trial.
"I welcome these culturally informed initiatives but I remain concerned about the conditions in which all remand prisoners are held.
"Remand prisoners continue to be double-bunked in cells built for one.
"The prison's lack of internal recreation space and purposeful activities means the majority of remand prisoners remain locked in their cell or in the yard, with few constructive things to do with their time."
The Chief Ombudsman made six recommendations, including improvements for general living conditions and better provision for prisoners with mental health issues, human rights, following the inspection.
The Department of Corrections agreed to address the issues raised, some of which were being addressed on a nation-wide basis.
In a statement yesterday Corrections said it was moving to standardise the serving of meals nationally through a review for shift patterns for staff in all prisons.
"When complete, this will hopefully go a long way to satisfying the concerns of the Ombudsman," said chief custodial officer Neil Beales
The Department also acknowledged concerns over prisoners in the ISU, and said it was working to address those issues.
"The prisoners in these units can be highly troubled and the preservation of life is Corrections number one priority," said Beales.
"However, I am leading a piece of work on this matter that will address those concerns while ensuring the safety and security of prisoners and staff is maintained."
