Mr Ellis' lawyer, Rob Harrison, said in a statement Mr Ellis, who had bladder cancer, died peacefully surrounded by family and friends.
He died while fighting to declare his innocence. He 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.
Whether it will go ahead or not appears uncertain.
A Ministry of Justice spokeswoman said yesterday that would be a matter for the court to consider in terms of any submissions that might be made on the issue.
Mr Harrison said he wanted to talk to Mr Ellis' family before commenting publicly on future options for the case.
Dunedin author Lynley Hood, who did extensive research and wrote a book, A City Possessed: The Christchurch Civic Creche Case, on the matter, said the Supreme Court case should continue.
Ms Hood said it was ''extremely important'', not just for Mr Ellis' reputation, but for the justice system as a whole, to continue with the case.
It had caused public disquiet for nearly 20 years, and the court needed to make a final call on whether a miscarriage of justice occurred.
''We have to be able to trust our justice system to get it right.''
Ms Hood said she had been in touch with Mr Ellis recently, having visited him earlier this year following his diagnosis.
It had been hoped he would survive long enough to see the outcome of the case, but that had not happened.
A team of University of Otago staff, including Vice-chancellor Harlene Hayne, as well as former law school dean Mark Henaghan, carried out research to get the appeal to the Supreme Court.
Prof Henaghan said yesterday the case, which was set down for November 11, should go ahead.
''It is a matter of quite considerable public importance as to how we go about these sort of cases.''
Any rulings would influence ''lots of other cases''.
''Cases such as this case, where you've got evidence from young children, are really important cases.
''There are quite a few lessons to learn as to whether we can do it better, and how it was done in this case.''
Mr 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, a ministerial inquiry in 2001 by Sir Thomas Eichelbaum 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.
- Additional reporting NZME
