Ellis was released from prison in 2000, after serving seven years for abusing seven children at the Christchurch Civic Childcare Centre in 1991.
The verdicts have always been contentious and in July, the Supreme Court agreed to hear the case once more. The approved ground of appeal was whether a miscarriage of justice occurred.
Whether the court case will go ahead or not following Mr Ellis' death appears to be up in the air.
A Ministry of Justice spokeswoman said that would be a matter for the court to consider in terms of any submissions that might be made on the issue.
His lawyer Rob Harrison said in a statement Ellis, who had bladder cancer, slipped away peacefully today surrounded by his loving family and dear friends Stephen and Pam Fergusson.
Ellis planned to be supported at the Supreme Court by a team of University of Otago staff who have done a vast amount of work on the appeal.
Speaking to Newstalk ZB's Mike Hosking last month, Ellis said the university had done a "wonderful job".
"There have been people who have been working at the coal face for nearly 27 years," he said.
Dunedin author Lynley Hood, who did extensive research on the case and wrote a book - A City Possessed: The Christchurch Civic Creche Case - said she would like to see the Supreme Court case continue.
Hood said it was "extremely important", not just for Mr Ellis' reputation, but for justice system as a whole, to continue with the case, as it needed to be decided if a miscarriage of justice had occurred.
She said the death was "tremendously sad".
It had been hoped he would survive long enough to see the outcome of the case, but that had not happened.
Mr Harrison, said he wanted to talked with Peter's family and have a discussion with them before commenting publicly on future options for the case.
Ellis twice appealed to the Court of Appeal, the second time after a referral by the Governor-General.
The first appeal quashed three of his convictions, but the second appeal against the remaining 13 convictions was dismissed in 1999.
After the second Court of Appeal decision there was a Ministerial Inquiry in 2001 by Sir Thomas Eichelbaum, which concluded there was no risk of a miscarriage of justice.
There have also been unsuccessful petitions to Parliament for a Royal Commission in 2003, 2008 and 2014.
With NZME
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Possibly the biggest blight ever, and there have been many, on the NZ justice system.
This witch hunt scared many men that would have been great teachers away from the career path.
Final Score Card
Homophobic pious intolerant bigots — 1
Justice for the individual ——————— 0
RIP Peter. You were a good man let down by a degenerate political system.
As in 'A City Possessed', it was a time of worldwide panic over "Satanic ritual", originating in the USA. There were quasi religious figures in Christchurch: a cosmologist 'Wizard', the public evangelist 'Bible Lady".
That psychologists bought into the Creche allegations reflects on the City at the time.
A miscarriage of justice does not start a pattern. No one can assert that, because of the Ellis case, all child complainants lack credibility.