Little also defended aspects of the authority that have come under criticism, including its proposed veto and funding powers.
"We have major equity concerns with Māori health outcomes, and the Crown has obligations under the Treaty, and the principal is partnership, offered here in terms of health administration and services."
These would be agreed at "locality level", he said.
"That is what a partnership arrangement looks like and I have total confidence whatever the process everybody be acting in the health system wants to act in the best interest of all New Zealanders."
When asked about the report and if he supported its recommendations Māori Development Minister Willie Jackson said he had read it and there were "recommendations the Government was already implementing".
Meanwhile National MPs backed Collins' decision to play the "separatism" card.
Collins used her speech at a regional party convention in Auckland on Saturday to issue what she called a warning Labour was leading New Zealand down a "dangerous path on race relations", warning of "separatism".
Deputy leader and the party's most senior Māori MP Dr Shane Reti said he supported Collins' comment.
"I believe the Govt with He Puapua indicating a separate sort of government, separate lifestyle, separate systems, I am concerned it is indicating some sort of separatism as Collins said.
"The He Puapua document has been kept undisclosed over a year, you have got to wonder why."
Asked about how then to address Māori inequities, which the report was designed to address, Reti said approaches should be "based on need".
MP Chris Bishop said Government actions were "certainly a form of separatism"
"I don't think it is helpful for the country, and delivering services for Māori."
Bishop said National was supportive of Māori aspirations to improve "appalling statistics" but ideas suggested in the He Puapua report were "certainly a form of separatism".
"The Government so far has been less than upfront on this and needs to be more transparent."
MP Nicola Willis said Collins had commented on National's support for the Treaty of Waitangi as the country's founding document, that breaches had led to the situation today, their support for the Treaty settlement process and a place for Māori-delivered services.
But the Government "owes New Zealand the opportunity" to discuss the latest report.
"It is very suspicious it has not been subject to public engagement.
"I would like to see the Prime Minister make it clear where she stands on the recommendations."
Speaking ahead of caucus, Collins reiterated her calls for the Government to be more upfront on the issue and her belief recommendations were already being implemented.
Asked about comments she was stirring up fear, playing politics and the "race card", Collins said New Zealanders "have a right to know what their Government is planning".
"Our constitutional arrangement is very important and does not mean the Government should by stealth just change it without getting consent of all New Zealanders.
"If we are to have major changes to the constitution they should be subject to a referendum."
