The wreck of the Rena will be allowed to remain on Astrolabe Reef after the Environment Court says everything that could be done has been done.

Judge Jeff Smith ruled out removing the stern and mid sections of the container ship that ran aground in the middle of the night of October 5, 2011.

He said the prospect of removing the deepest stern section was negligible and it should be left in situ to flat-pack, or collapse into itself.

He accepted evidence from Joe Te Kowhai, the diver used by Rotorua pan-tribal authority Te Arawa, that the use of grapples and chains to remove the 600 tonne mid-section of the wreck would have a "significant adverse impact on the reef".

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This left the bow or front section of the Rena that was embedded in the top section of the reef below the water line.

Judge Smith said the wholesale removal of the bow, including pieces that had gone over the reef, was "not appropriate". However he signalled that the Bay of Plenty Regional Council should have the power to order the removal of parts of the bow that broke away.

"Similarly, we consider that provision should be made to consider the removal of contaminants TBT and copper, if circumstances arise where it is both feasible and safe."

The court was ruling on the appeal against the 2016 decision by the regional council to leave the remains of the Rena on the reef.

The appellants were Motiti Island's Ngai Te Hapu and Papamoa hapu Nga Potiki. Maketu's Ngati Whakaue and Te Arawa Takitai Moana Kaumatua Forum joined Nga Potiki's appeal.

Nga Potiki's lawyer, Tama Hovell, was disappointed with the outcome of the appeal and said he was still analysing the decision which would need to be considered by the iwi.

Mr Hovell said there were positives and negatives, including recognition of the tangata whenua groups with primary connections to Motiti. "We are not including ourselves in that."

The court made an interim decision, leaving it up to all the parties to consult on the conditions of consent. The parameters of the conditions of consent were set out in the decision.

Lawyer Matt Cassey, QC, representing the Astrolabe Community Trust that applied to leave the remains of the Rena on the reef, said the court had largely dealt with the impact on the mauri of the reef - its spiritual wellness or life force.

Mr Casey said the decision dealt with the potential effects of what was left, monitoring the effects, and the formation of the Kaitiaki Reference Group comprising representatives of the principally affected Maori groups.

"It was a very positive decision in terms of charting a way forward."

Ngati Whakaue lawyer Robert Makgill said the court had come out strongly and said all affected iwi needed to be dealt with, even if they were not submitters to the application.

He said the decision inserted environmental triggers into the original monitoring conditions so that if triggers were reached then action was required. The original consent only required monitoring of what the applicant's experts anticipated would happen, with no requirement to take steps to mitigate or remedy any adverse effects that were not anticipated.

A further appeal to the High Court must be on questions of law.