A misconduct charge could be for something like fighting, having contraband or deliberately damaging prison property.
In the past year, 2019-2020, more than 21,000 charges were laid against prisoners.
But across that time, 8617 or 40 per cent were cancelled.
A charge can be dropped if it is not filed within seven days of a staff member learning of the incident or if an adjudicator cannot hear it within 14 days.
Corrections Association president Alan Whitley said time and staff limits were undermining efforts at discipline.
"The internal disciplinary system is in dire straits and it needs some action. It's an example of an erosion of trust of the staff and the systems there to look after them.
"If they are consistently seeing charges dismissed because they are out of time, it says to them, no one really cares that they've actually raised the matter and that they're trying to hold prisoners to account."
Whitley said corrections officers were not resourced properly and prisoners recognised they could get away with bad behaviour.
"Since about 2017, we've had a softer and softer and softer approach to prisoners.
"And since 2017, the incidences of violence against staff have increased.
"The prisoners basically know that they've got a good chance of getting away with what they do and they'll just continue to push the boundaries."
In the 2019-2020 year 889 officers were assaulted. That was sharply up from 654 the year before.
Boss agrees system not working
Corrections chief custodial officer Neil Beales said there were many reasons charges could be dropped but admitted the system was not working.
"If I thought it was good enough, I wouldn't have just employed a principal advisor in my team to oversee this specifically for me as part of the violence and aggression action plan.
"The adjudication and prosecution system has been around for a very, very long time. But clearly it's now due for us to take a good long look at it to see whether it's still fit for purpose."
Neil Beales agrees Corrections needs to decide if the system is "still fit for purpose". Photo / RNZ, Claire Eastham-Farrelly
The new principal advisor has started in the job and had scheduled more training for officers in September.
Beales said one problem was that adjudicators are often the first people pulled off shift to cover gaps elsewhere.
But he warned it was not just about staffing.
"So it's a very, very complex thing and it would be wrong for me to say that there is just one thing that causes this system to fall over.
"It's a multitude of things, which we have to get on top of as a department and we need to make sure that we've got a good line of sight on what's happening with our adjudications and prosecutions on any given day."
The new advisor would check if there were enough adjudicators at each prison as well as review Corrections law and individual prison policies.
"Part of running a safe and secure prison is by having a disciplinary system that is lawful, is fair, is transparent, and it works.
"People understand why it works, it can be scrutinised, there's an appeal process involved.
"All of the normal things that you or any other citizen would expect to see. And that's what they want, and that's what we need to give them."
Beales said the department also wanted to investigate if the type of punishments was appropriate.
Currently, an adjudicator can give anything from a warning to cell confinement, loss of privileges or up to $500 in reparations - in serious cases charges are referred to police.
Advocate says system fails inmates, staff
JustSpeak director Tania Sawicki Mead said the current punishment system did not keep inmates or staff safe.
"Nothing in the way that the system is being run actually gets good outcomes for people there.
"It is not a place built around policies that enhance safety or wellbeing, whether it's for people working there or people being held there.
"And the long term consequence of that is that people are not actually getting the help that they need, and we're not doing anything to resolve the fundamental drivers of people going into the justice system."
