Too few toilets were provided, he said.
"The people who are in there have done nothing wrong. They are mentally unwell, acutely unwell. They are there usually because a detention order has been made.
"On one occasion, just before my inspectors were there, nothing was available and unfortunately one of the service users just had to pass a bowel motion in the corridor.
"Pretty degrading and not that good for someone who's trying to therapeutically get better with their mental wellness."
Boshier said seclusion rooms were intended for use only when patients needed to be kept apart to protect themselves or others, but were often used as bedrooms.
Unlike the more "welcoming" bedrooms, seclusion rooms had no toilet or other basic necessities, he said.
"There aren't enough bedrooms.
"When my inspectors go through, [seclusion rooms] are more often than not being used as bedrooms.
"These rooms are hardly therapeutic... It has nothing in it.
"This should not be used as rooms for people who don't want to be there, have to be there, and are trying to get better."
Boshier said New Zealand had fallen below the standards required in the United Nations Convention against Torture and Other Cruel, Inhuman or Degrading Treatment or Punishment.
He has repeatedly made recommendations that facilities need to be improved to meet UN standards.
"In most aspects of a hospital which the public get to see, like maternity and like orthopedic, they are kept modern and they are kept clean.
"The reason we are keen to highlight these in our inspections is because the public generally does not get to see and generally does not therefore know.
"I just hope there's a groundswell of support for doing better."
Following an unannounced inspection last year at STAR 1 mental health facility at Palmerston North Hospital, the ombudsman found personal restraint and medication were used too often to de-escalate patient outbursts.
STAR 1 had an "institutional" atmosphere, an "unsafe" outdoor space, and patients' movements were restricted by staff sitting in the doorways of their rooms, the report said.
Boshier said the mental health unit, Tiaho Mai, at Middlemore Hospital in Auckland opened two years ago and was the best of the three facilities inspected.
"You walk in through a marae type setting, very welcoming, you feel like you're waking into a therapeutic, nice environment."