The reef's ecosystem has since begun recovering, but the applicants wanted limits on fishing to allow marine life to return to pre-shipwreck levels. The Bay of Plenty Regional Council said it did not have power to prevent fishing around the reef, but the Environment Court ruled that it did.
Green Party environment spokeswoman Eugenie Sage said the ministry itself should be protecting the reef and other maritime areas. Instead, it was blocking local communities from protecting their own backyards, she said.
"If MPI won't use its powers to protect the Otaiti (Astrolabe) Reef or other significant marine areas from fishing pressure then hapu, iwi and community organisations should be able to ask their regional councils to use the RMA and regional coastal plans for help.
"Now having failed the local community, MPI wants to block off that option too."
Forest and Bird spokesman Geoff Keey accused the Government of "road-blocking" councils from protecting the marine environment.
"The Environment Court offered our oceans some hope last year, by confirming that regional councils can regulate fishing and marine activity to protect New Zealand's underwater ecosystems," Mr Keey said.
"Finally someone could do the crucial job that central government has been ineffective in doing themselves."