These included the case of Ashley Peacock, a 38-year-old autistic man held for five years in the isolated ward of a mental health unit, and who has experienced periods of prolonged seclusion, the medical term for solitary confinement.
His living conditions - he sleeps in a seclusion room with just a mattress and a urine bottle - were recently labelled "cruel, inhuman or degrading" by Chief Ombudsman Peter Boshier.
Last week, it was revealed there were three other cases also in that category at secure health facilities around the country, including dementia units and forensic mental health wards.
The Human Rights Commission, concerned by the ongoing issues in the sector, plans to bring an expert in seclusion and restraint to New Zealand - with funding from the United Nations - to investigate.
Meanwhile, the Ombudsman's Office is considering an investigation into health and disability places of detention, which it is responsible for monitoring under the Crimes of Torture Act.
Central to all of the cases are patients with high and complex needs - a group repeatedly highlighted by experts as needing better, specialised care and housing.
These usually involve people with both mental health and intellectual disability issues, or behavioural problems who pose unique challenges to the system and can be expensive to look after.
The three men taking action against the Government have intellectual disabilities. One is autistic. They were all committed as special patients after coming before the courts on violence charges around 15 years ago, when they were found unfit to plea.
All have spent significant periods - up to 18 years in one case - in secure units. They allege a raft of ill treatment occurred in the facilities, from prolonged and inappropriate seclusion to a lack of rehabilitation, or "warehousing", to sexual abuse.
The Attorney-General and the two health boards will be accused of "failing to treat the applicants with autonomy and dignity". The other two defendants are the District Inspector and the Mental Health Review Tribunal.
Human rights lawyer Dr Tony Ellis will bring the case on behalf of the men.
The health boards named in the judgment are Waitemata and Capital & Coast, which run specialised forensic intellectual disability units and mental health wards.
The health boards declined to comment while the case was before the courts. The Ministry of Health also refused to comment.