Commission chairman Judge Gordon Whiting said the change of heart by iwi, who agreed to the restoration and mitigation funds, had a mixed reception.
Dr Young said a significant question faced by kaitiaki (iwi, hapu and kinship groups) was whether removing the wreck would damage the reef more than leaving it there.
He said, if consent was granted, then removing the bow sections of the Rena higher up on the reef would reduce the impact on the mauri. "I do not consider the impact of the proposal on cultural values to be minor."
Judge Whiting said he was not sure how they would resolve the complex Maori issues, saying it was a "complex landscape" in the Bay of Plenty.
Each Maori group may have a relationship with the reef that, while similar in name, may differ. He asked whether the commission should look at each group separately and try to determine what values were affected, and make determinations for each group. Dr Young said the consultation process did not take account of the people who did not want to participate or go through consultation that involved a third party - the applicant.
It was not uncommon in consultation processes for difficulties to arise between iwi and hapu, he added.
He said the different conclusions reached between iwi and hapu were because of the way the engagement process had been run.
Consultation had been thorough but he still had "very serious concerns".
Judge Whiting said the divergence of views was understandable but no one had suggested conditions to alleviate the hurt to Maori values if the application to leave the Rena on the reef was granted - once they had listened to each Maori group.
They could not take the conditions of those who had agreed to take part in consultation and apply it to those that did not take part, he said.
Dr Young said the values of those that did not take part could not be marginalised from the decision-making process. Consultation had been very broadly defined.
Ngati Makino Trust speakers, including Te Ariki Morehu, Raewyn Bennett and Joe Te Kowhai, spoke on behalf of Te Arawa of their support for the resource consent to leave the MV Rena on the Astrolabe Reef, at yesterday's hearing.
Kaumatua Te Ariki Morehu said his iwi took the advice of their divers to support the resource consent.
New round of talks ordered
A new round of negotiations has been ordered by the commission hearing an application to leave the wreck of the Rena on Astrolabe Reef. Chairman Judge Gordon Whiting said he was about to issue a memorandum for the parties to the application to "caucus".
One of the questions was should clear conditions be set out in matters of consent. His comment came during evidence at yesterday's hearing by expert Crown witness Mark Ashby.
Mr Ashby argued that consent conditions needed to be beyond legal challenge. He said the applicant sought to limit the application to contaminants still within the wreck.
"In doing so, it seeks to exclude any ongoing discharge from contaminants not within or on the wreck, but which were released during the grounding or in the aftermath as Rena broke up."
He said the applicant considered the contaminants were part of the existing environment, and so were only relevant as a baseline to measure additional effects.
Mr Ashby supported removing the Rena's bow sections in order to limit future damage to the reef and its ecosystems.