One hundred young people have run away from Oranga Tamariki Care and Protection Residences since 2016, the youngest being just 10 years old.
The residences are designed to hold and protect at-risk young people in state care, who have not committed a crime.
More than 40 broke out on a weekend or during the school holidays, which were times they were more likely to be accessing community activities.
Assistant Māori children's commissioner Glenis Philip-Barbara said the figures showed the residences were not meeting the complex needs of young people.
"Whether there are two young people absconding, or 100 over a specific period of time... this is children communicating with us about needs that are unmet," Philip-Barbara said.
The rangatahi housed in the residences were mostly Māori who had been disconnected from their culture due to time spent in state care, she said.
A report from her office in 2017 described the majority as also being "exposed to serious physical, sexual or emotional abuse within their families or whānau".
Philip-Barbara said they were placed in the residences because all other avenues in state care were no longer available due to their needs.
But the environment did not help to improve their mental state, she said.
"In these kinds of places where children and young people are fearful, both of the other young people in the residence, and you know, other worries and behaviours, you can't actually generate an environment for healing or restoration in such a place."
In a statement Oranga Tamariki spokesperson Audrey Bancroft said staff were dedicated to keeping young people safe while promoting well-being.
"At times young people have left our care from a community setting while on appointments, organised outings, sports or otherwise away from a residence," Bancroft said.
"They may be out of contact from us for a very short period of time.
"Residences have good processes around debriefing and learning from when such incidents occur."
Bancroft said the agency was working to establish new and smaller community-based homes over the next five years.
That would be the first step towards developing a range of placement options allowing for transition away from the residences, she said.