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This week separate company Trans-Tasman Resources had its second application - to mine 50 million tonnes of sands off the Taranaki seabed, in order to sift out 5 million tonnes of ironsands for export annually - overturned.
Chatham Rock wants to suction up 1.5 million tonnes of phosphate nodules from the Chatham Rise seafloor, about 250km west of the Chatham Islands, in depths of up to 450m.
What was successfully overturned by the High Court was the EPA's granting of marine consent to Trans-Tasman last August to mine within 66sq km of the South Taranaki Bight for 35 years.
Trans-Tasman Resources has now twice had its bid rejected, and could yet appeal the latest decision, while Chatham Rock's first marine consent application was rejected in February 2015.
Environmental and fishing groups, iwi and communities had challenged the Trans-Tasman marine consent in the High Court, which this week quashed the decision, saying an "adaptive management" approach did not protect the environment adequately.
Despite the setback for Trans-Tasman, Chatham's chief executive Chris Castle said the High Court decision of Justice Peter Churchman would provide "important precedents for future marine consent applications".
While Justice Churchman found the EPA decision-making committee was not permitted to use an "adaptive management" approach, Mr Castle said comments by him "appear to support implementation of adaptive management".
He believed Justice Churchman's decision provided a "comprehensive platform" to support the "prompt amendment" of the Exclusive Economic Zone (EEZ) Act, which would bring it into accord with other domestic and international legislation.
Chatham already has a mining licence for the Chatham Rise and is now working through its marine consent reapplication.
Mr Castle said yesterday he expected to file a "scoping review" to the EPA in November.
Kiwis Against Seabed Mining (KASM) and Greenpeace welcomed the Trans-Tasman decision as a "victory for the oceans" and the 13,000 submitters on the project.
KASM chairwoman Cindy Baxter said the main part of the decision by Justice Churchman focused on "adaptive management".
She said it was a practice of "trying it out and seeing what happens, and adapting the conditions accordingly" which was argued as illegal under New Zealand law applying to the EEZ and continental shelf.
Fisheries Inshore New Zealand chief executive Dr Jeremy Helson said Trans-Tasman's most recent application was almost identical to the first, and did not address the EPA's key reasons for refusing its application in 2014.
"It is clear from these [three] failed attempts that a significant re-think is required on seabed mining," Dr Helson said in statement.
He said the High Court quashed the decision, saying the narrow interpretation of the adaptive management approach was inconsistent with the law.
"This is a good decision by the High Court and we are pleased this matter has again been rejected," Dr Helson said.