In the judgment today, it said one of the concerns was around the reliability of the evidence.
It said one detail gave them "cause for caution" about the statement that Ellis was the perpetrator.
The woman said she realised for the first time in 2007 that Ellis was the person who had sexually abused her.
This was inconsistent with what she said in an evidential video interview in 2019 that she felt guilty seeing reports of Ellis's case because she had not made a complaint, the judgement said.
"She could only have felt that guilt if she had been aware at that time (1993) that the appellant was the perpetrator. It also raises a concern that this may have triggered an incorrect recollection."
Another concern for the court was the "unfairness" to Ellis that the allegations could not be put to him.
"Even putting to one side the impact of the allegations not being put to the appellant on the assessment of the reliability and relevance of the proposed evidence, there is a simple question of fairness in admitting the proposed evidence in circumstances where the appellant did not have the chance to respond to the allegations, creating a risk that this would unfairly prejudice his appeal."
Ellis was convicted on 16 charges of sexual offending against seven children in 1993.
He appealed twice to the Court of Appeal, the second time after a referral by the Governor-General. The first appeal quashed three of the convictions.
The second appeal against the remaining 13 convictions was dismissed in 1999 but Ellis was granted leave to appeal against the remaining convictions by the Supreme Court in 2019.
Ellis died in September 2019 but the court decided the appeal should continue.
In the judgment today, it said the decision to rule the new allegation as inadmissible as evidence focuses only on the integrity of the inquiry in the appeal.
"We do not and cannot have any view about whether the deponent's allegations are in fact correct.
"We see nothing to be gained in deferring our decision until the hearing of the appeal. That would prolong the proceeding and would potentially require the deponent to be cross-examined unnecessarily, in circumstances where we see very little prospect that our assessment of the admissibility of the proposed evidence would be any different."