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The decision marked a decade-long fight over land use in the Mackenzie Basin.
The Environment Court heard the matter, brought under the Resource Management Act, by various appellants including Federated Farmers of New Zealand, in January and February. Final submissions were received in March.
Mackenzie Mayor Graham Smith was relieved a decision had been made and said it meant the council could move forward.
He acknowledged some people would not be happy with the decision, but it could be challenged within 30 days of its April 13 release.
He said plan change 13 had so far cost the council more than $1million.
Originally the plan was about restricting fragmented growth in Mackenzie.
''That was the basis for our original plan change. That was challenged because farmers thought they had been given freehold land. They thought they had the right to do what they wanted on freehold land and I sympathise with them.''
Judge Jon Jackson said in his report there was quite a strong ecological and economic case for an immediate moratorium by the Commissioner of Crown Lands (CCL) on further freeholding of any land in the Mackenzie Basin containing ''outwash gravels''.
A table in the report from evidence presented on behalf of the Department of Conservation detailed indigenous vegetation remaining on naturally rare ecosystems in the Mackenzie Basin and extent of their loss.
It showed that between 2000 and 2016 the Omarama ecological district suffered a 47% loss of its alluvial outwash gravels (AOG).
The Pukaki ecological district had lost 21% AOG and Tekapo's ecological district lost 13%.
The same table showed Omarama again losing out, this time with its moraines.
From 2000 to 2016 it had lost 37% of its moraines, Pukaki 22% and Tekapo 8%.
Judge Jackson said during the moratorium a comprehensive ''all-station'' review should be carried out and a plan formulated including the council's review of Rural Policy 1A and its implementing methods.
''In particular, any of the stations with pastoral leases contained 'outwash gravels' need to be looked at very carefully.''
Judge Jackson added the court accepted the Mackenzie Basin Subzone Boundary should be specifically identified on planning maps as an ''outstanding natural landscape''.