Mr Ellis' lawyer Nigel Hampton QC, said his client would be "somewhat disappointed" by the decision.
"But it doesn't shut all the avenues, he's still got the ability to appeal to the Privy Council. And the other principal alternative is to again renew an application to the Governor-General for the exercise of the Royal Prerogative, which would lead, if successful to a further hearing in the Court of Appeal," Mr Hampton said.
"Those are the two avenues open to him still, and they are the ones that we will be discussing with him and deciding on in the next little while as to which avenue we'll follow."
It would be two to three months before the team make a decision, he said.
The case was a "political hot potato" that successive ministers had tried to avoid, Mr Hampton said.
"I think it's being seen in very narrow terms, and conveniently so," he said. "I think politicians regard this as rather a hot potato and they'd rather not have their hands on it."
He added: "It's been on the desk of I think about seven or eight Ministers of Justice and it's seen as being a political hot potato and the less a minister has to do with it the better it is from that minister's point of view. So this [decision] really follows a pattern of previous conduct and attitude towards applications by Ellis or on his behalf."
Despite that, Ellis was "still hopeful that at some stage in his lifetime his position will be vindicated and his name will be cleared", Mr Hampton said.
Dunedin author Lynley Hood, who wrote the award-winning A City Possessed: The Christchurch Civic Creche Case, which looked at the Ellis case, said the decision by Ms Adams went to the heart of what is wrong with the New Zealand justice system.
"It's very disappointing," she said of the decision. "And it's just another example of how the justice system seems incapable of recognising and correcting its own mistakes."
Releasing her decision today, Ms Adams said she considered the public interest and legal issues before declining the request for an inquiry. She also said Ellis had not exhausted his right to appeal.
Dr Hood however, described this as a "cop-out".
"The legal options never end, and this is part of the cop-out that the justice system uses when they say he has not exhausted his legal options," she said.
"You can apply multiple times for the Royal Prerogative and go to the Privy Council, but they tend to get narrower and narrower, and they're just saying, 'where's the new evidence?', and the problem with the Civic Creche case is there was no reliable evidence in the first place.
"There have been numerous calls, including petitions to Parliament that were supported by a huge weight of legal authority, for a Commission of Inquiry led by an overseas judge to examine the whole case from beginning to end, because if you're just looking for new evidence you can say, 'well we looked at that back at the trial', and so on, so you have to have fresh eyes looking at it and saying, 'they got that wrong'.
"People have to learn from the mistakes that were made, and they never will if they pretend they can fix the problem by finding a piece of new evidence and saying, 'oh if we'd known that this would never have happened'. That's rubbish, because all sorts of things went wrong all the way down the track."
The request for the inquiry was made by Dr Hood and former leader of the National Party Don Brash.
