The Ministry contracts five District Health Boards to provide forensic intellectual disability services. The DHBs provide around 66 secure hospital beds nationwide.
Boshier's investigation would look at whether the facilities were adequate for those referred by the courts for assessment as well as for long-term clients, women and youth.
He will also examine how much workforce planning is being done to make sure there were enough appropriately trained staff.
He will conduct a separate investigation into the quality of the data collected by the Ministry relating to the deaths of intellectually disabled people in forensic and residential care.
"I consider that obtaining good quality data is essential to understanding where the pressure points are and for reviewing systems of care," Boshier said.
"I want to ensure that the Ministry is collecting enough information about these deaths to identify whether any improvements can be made.'
The investigations follow years of concern about the system, including the treatment of complex clients like Ashley Peacock, who was locked in seclusion for more than five years despite evidence it was not helping his health.
Last year, the Herald reported women with intellectual disabilities were sharing bedroom corridors with "predatory" men as the Mason Clinic hit capacity.
Health bosses wrote a pleading letter to the ministry, describing a "severe" situation needing urgent attention.
The investigations would be conducted under the Ombudsmen Act.
They reflect the Ombudsman's role in protecting and monitoring disability rights in New Zealand, and contributing to systemic improvement by investigating public sector administration and decision-making.
Boshier said he would also be taking the United Nations Convention on the Rights of Persons with Disabilities into account.
The investigations will include site visits and one-on-one interviews with clients in the secure facilities, their families/whānau, as well as officials, medical professionals and other stakeholders.
People who wish to raise concerns about their individual circumstances can continue to do so at:
http://www.ombudsman.parliament.nz/make-a-complaint/make-a-complaint-now/make-a-complaint-online-now
The investigation relating to data around deaths of people with intellectual disabilities in residential and forensic care will be completed in the second half of 2019.
The investigation into facilities and services for intellectually disabled people with high and complex needs is planned for completion in the first half of 2020.