"A recent example of which I am aware is a Corrections approach to Ministry of Justice officials which led to priority being given in scheduling of cases because of a problem Corrections had in providing female remand beds.
"The inappropriateness of this sort of private adjustment seems not to have been understood. There is a risk of breakdown in understanding of proper boundaries."
The number of female remand prisoners has almost doubed in the past three years, outstripping steady growth across the entire prison population
Corrections figures show that in March 2014 there were 110 women in prison on remand, meaning they had yet to have their charges completely dealt with in court.
The most recent figures in March 2017 showed the number in prison on remand had grown to 220 women.
Over that same period, the entire prison population had grown from 8520 to 10,035 with the total remand population growing from 1802 to 2892.
Corrections Minister Louise Upston said reasons the prison population had increased included a 2013 law change made it harder for people charged with serious offences to get bail.
She said efforts to manage the number of remand prisoners included "speeding up court processes, assisting people to apply for electronically monitored bail and helping with support and appropriate accommodation in the community".
Corrections deputy national commissioner Leigh Marsh confirmed there were efforts to help prisoners access their right to electronic bail.
It was part of trying to cope with a prison population which had exceeded forecasts, she said.
Extra space had been found in seven prisons through double-bunking and reopening units previously closed along with rapid deployment of three sets of 120-prisoner units at two prisons.
"In addition, we have a programme of work underway to ensure those in custody who are eligible to apply for EM (electronically monitored) bail or home detention, are supported to do so.
"Some of the reasons these options may not be applied for include lack of literacy or an inability to investigate potential suitable and safe addresses to reside at, so our staff currently have an increased focus on ensuring that offenders and defendants are supported in these areas."
CANZ president Alan Whitley said the "Enhanced EM Bail" team was initially focused on female remand prisoners because that sector of the prison population was approaching capacity.
"We're in a situation where we have more prisoners coming into prisons than we have room to house them. We're getting pretty tight at the moment. We don't have a lot of breathing space."
Labour Party deputy leader and Corrections spokesman Kelvin Davis said it should not take a lack of space for prisoners to create a situation which allowed some inmates to access their legal rights to electronic bail.
The initial narrow focus on female inmates ties in with the concerns expressed by the Chief Justice as it would have seen those prisoners getting a different access to justice than male remand prisoners.
The Bill of Rights gives defendants "the right to be tried without undue delay". In legal circles, leapfrogging one class of prisoner before another for administrative purposes - clearing cell space - would cause an uproar.
The Chief Justice's speech - given at the Criminal Bar Association Conference - reflected the tension between the nation's court system in which the judiciary hear cases and the government, which appoints the Ministry of Justice to handle the non-legal administration.
There is meant to be a clear separation between the courts system and government - with Parliament as the third branch of state - but there is concern among the judiciary that the gap between the two is blurred in places.
The tension became exacerbated when the previously-separate Department of Courts - over which judges had greater sway - was brought under the Ministry of Justice.
Elias told the conference: "There is little agreement about where judicial administration takes over and Ministry administration leaves off.
"These matters of separation were flagged as problems from the time the Ministry of Justice took over the Department for Courts.
"They have become acute because of the erosion of the culture of courts within the Ministry."
