Amnesty International New Zealand executive director Grant Bayldon said everyone had a right to humane conditions of detention.
"We are concerned at these findings from New Zealand prisons. It shows that nowhere in the world, not even in New Zealand, are people totally free from the risk of torture and other ill-treatment."
Bayldon said the Government had a responsibility to respect, protect and fulfil human rights.
"This includes taking effective steps to prevent acts of torture and other ill-treatment."
He said all complaints or reports should immediately be investigated, and "those responsible held to account".
Greens Corrections spokesman David Clendon said the findings were "nothing new, sadly", but the corrections system had to change.
He said the reports shed light on the penal system's faults.
"I think it reveals that the dysfunction in our corrections system is pervasive...There are serious human rights shortcomings, and it shows our system is not working. We're making prisons less safe for the staff too."
A spokeswoman for Corrections Minister Judith Collins said Corrections took its duty of care towards prisoners seriously.
It was committed to managing all prisoners in a safe, secure, humane and effective manner.
"Prisoners have the right to be treated with humanity, dignity and respect while in prison, therefore there are a number of human rights standards in place to ensure safe detention."
In the case of the Otago inmate restrained for 21 hours a day, the spokeswoman said the prisoner had carried out nine self-harm attempts and been admitted to hospital on several occasions with injuries.
"It is likely he would have died had the prison not taken these steps.
"The Prison Director sought multi-disciplinary advice on how to manage this prisoner safely and humanely, including consultation with the Southern District Health Board's Mental Health team.
"A carefully considered management plan for this prisoner was created and this included restricted use of waist restraints."
The spokeswoman said many of the recommendations made by the Ombudsman had already been carried out, and Corrections was continuing work to progress recommendations that require action. Some recommendations were not accepted.