Objections from Maori groups about selling public electricity companies that rely on water power was heard in the Waitangi Tribunal and High Court, and has reached the Supreme Court.
"It's a topical issue and suggests relationships aren't as good as they really are," Dr Moon said.
"People don't see, perhaps, the cases where trust boards have made settlements with the Crown and are now making jobs and getting involved in development. You don't always see that for the crisis points.
"I think there's a very good, strong and enduring relationship - much healthier than it was 30 years ago."
The year had been the beginning of the end of Treaty settlements for historical claims, Dr Moon said.
"The process began in the 1980s - and for a whole generation of New Zealanders who have lived through it, it's drawing to a close. Bit by bit the loose ends are being tied."
The quality of settlements had also broken new ground. The Crown's settlement with Tuhoe showed a genuine commitment to working together on social services and managing national parks, Dr Moon said.
"The Government isn't just throwing money and hoping the problem goes away.
"It really rejuvenates the relationship. Instead of being about stale, historical claims it becomes a vibrant partnership."
Dr Moon said he was not surprised by the poor public perception of the Treaty relationship.
"There's never been overwhelming enthusiasm for the Crown and Maori relationship."
Race Relations Commissioner Joris de Bres said that being disapproving of Treaty relations was the one thing that brought all groups together - pro-Treaty, anti-Treaty, pro-Government and anti-Government.
"People are united in this one thing - that it isn't good enough," he said.
"That's reality. We're not at the point that everybody has a good sense of indigenous rights and Treaty rights.
"Race relations in New Zealand is a journey.
"But given that we continue to make progress, over time people will come to embrace the outcomes."
There had been big shifts in society, particularly around embracing Maori language and culture.
And last year had seen phenomenal achievements between Maori groups and the Crown, he said.
"The standout was persistent, significant progress in Treaty settlements. It's realistic now that by the end of 2014 everything will be wrapped up."
But the gains also extended to aquaculture, fisheries, park reserves and other partnerships.
"We've come a huge way in the last little while. We've had some setbacks, but I would say that overall the trend is positive."
The poll's sample size was 750, with a margin of error of 3.6 per cent.
Treaty relations
Poll: "The Treaty relationship between the Crown and Maori is healthy."
2008 40 per cent agree
2009 28 per cent
2010 26 per cent
2011 25 per cent
2012 23 per cent
Source: HRC
Progress in 2012
Signed deeds of settlement
Te Aupouri; Tamaki Makaurau Collective; Ngati Raukawa; Ngati Ranginui; Ngati Rangiwewehi; Tapuika; Ngati Toa Rangatira; Ngai Takoto; Te Rarawa; Ngati Koroki Kahukura; Ngati Koata; Te Atiawa o te Waka-a-Maui
Bills introduced but not yet passed
Ngati Whatua o Kaipara; Waitaha
Legislation passed
Ngati Pahauwera; Ngati Porou; Nga Wai o Maniapoto; Ngati Whare; Ngati Manawa; Rongowhakaata; Ngai Tamanuhiri; Ngati Manuhiri. Maraeroa A and B Blocks. Ngati Makino. Ngati Whatua Orakei
Plus 13 groups involved in terms of engagement, deeds of mandate, terms of negotiation, agreements in principle, high level agreement or initialled deeds of settlement
