Chief Ombudsman Peter Boshier is investigating how the Department of Corrections is responding to repeated calls for reforms aimed at improving conditions for prisoners.
The way prisoners are treated has come under closer scrutiny since the riots at Waikeria Prison over the New Year.
"In many areas, I have not seen significant and sustained improvements to prisoners' welfare and rehabilitation," Boshier said.
"This is despite concerns about conditions being raised by me and others at different levels of the department, and report after report being released calling for change.
"I simply want to know why."
Among the high-profile incidents that prompted him to carry out the inquiry now was the handcuffing of pregnant prisoners just prior to giving birth.
"You would have thought that a number of practices are inhumane and shouldn't occur and yet it's taken media last week to highlight a practice and hey presto, policy announced yesterday that it would stop", he told Morning Report.
"I want to know what the forces are at work that stop good things happening."
"When I looked at successive prisoner reports we've done, and I look at the number of repeat visits and repeat follow up recommendations, and the fact that it's been hard to get traction - I don't have that problem with other agencies.
"I found it much more difficult in Corrections.
Boshier said he would like a change in attitude from the department. Corrections was "fiercely defensive" of the use of tie down beds, but two years after his 2017 investigation their use was banned.
"I'd like there to be an attitude of more willingness to look and say 'why not' rather than 'why'."
Boshier expected the "independent, wide ranging" investigation would take a year to complete.
"I want to find out why problems continue to exist across the whole prison network and how the department is genuinely taking action to address these."
"I have become increasingly concerned about seeing the same issues coming up time and time again," he said.
Māori Party co-leader Rawiri Waititi, who in February called for a ministerial review into inmates' treatment, welcomes the investigation but said it was hard to feel optimistic that it would result in systemic change.
"How many reviews and reports does the minister, the CEO and this ministry need before there is transformative change in this particular space?"
People Against Prisons Aotearoa spokesperson Emilie Rākete said the investigation had been a long time coming especially given flaws at Waikeria Prison had been made clear in an earlier report.
Corrections Minister Kelvin Davis welcomed the investigation, while noting that Corrections' strategy to improve outcomes from prison, Hōkai Rangi, is only part way through its introduction.
"People need to realise there have been substantive changes in Corrections already over the last three years, and we're less than two years into a five-year strategy, Hōkai Rangi.
"There's been a lot of change in those less than two years with the Māori pathways that have been launched and other parts of Hōkia Rangi."
Department of Corrections chief executive Jeremy Lightfoot said in a statement he met often with the Chief Ombudsman and this investigation had been an ongoing topic of discussion.
"It is critical that we are open to scrutiny and I have advised the Chief Ombudsman that we will do everything that we can to ensure that he and his team have access to whatever they need from us."