A trial date has been set down for May 17 next year.
The officers were remanded on bail, with a case review hearing scheduled for August 26.
The three officers sat together quietly in the dock throughout the hearing, with the public gallery behind them packed with supporters.
Outside the courthouse, a lone anti-police protester stood with a placard.
Police said the decision to later file charges was made after a thorough investigation and consideration of legal advice from the New Plymouth Crown Solicitor and a Queen's Counsel.
Police weren't commenting further on the case as it was now before the courts.
All three officers have been stood down from their duties, with an "employment process" to follow in due course.
Police Minister Stuart Nash this month said any incident involving a loss of life in police custody was taken very seriously and the charges reflected "the gravity of the circumstances".
"This will be a difficult time for the victim's family and the wider police organisation. I extend my sympathies to the man's family.
"It is also important to acknowledge the professional work by a police investigation team to get to this point."
The Police Association has urged people not to speculate about the case - and said there was no suggestion that the death was the result of any physical or violent confrontation between the officers and the deceased.