Retired Mount Maunganui lawyer Rob Paterson, who submitted to the ministry against the trust's application, said he was heartened by Mr Guy's decision.
"In a nutshell, it is a victory for recreational fishermen and the average Kiwi."
Mr Paterson said the decision was logical and represented common sense.
Mr Guy's ruling against the application made under the Fisheries Act now left the trust relying on a High Court decision to achieve its goal of introducing fishing controls on and around the reef.
The trust and Forest and Bird have used a different legal pathway to try to achieve the same result, this time relying on the Resource Management Act instead of the Fisheries Act. They successfully appealed to the Environment Court on the Bay of Plenty Regional Council's ruling that it did not have the power under its Coastal Plan to control fishing.
The Environment Court ruled that the council could place restrictions on fishing. This decision was challenged by the Crown, with the issue ending up in the High Court in Hamilton last month.
Lawyer for the regional council Paul Cooney said a decision was expected by the end of this month. The council joined the Crown's appeal, saying it partly supported the Crown's position.
Mr Cooney said the council argued it did have power under the Resource Management Act to control fishing, but only where the purpose was clearly a resource management purpose.
The Bay of Plenty Times' request for a copy of Mr Guy's full decision resulted in ministry officials putting the request into an Official Information Act process.
Trust chairman and Motiti Island kaumatua Umuhuri Matehaere said they suspected that the ministry was not going to agree because it took so long to get a response.
He said the ministry was not quite sure how to deal with the trust because it seemed to think it was not an iwi organisation. All the trustees were born and raised on Motiti Island.
''We are an organisation that advocates for what needs to be done around Motiti.''
Mr Matehaere said that since the exclusion zone was lifted around the reef, ''every man and his dog was at the rock fishing''.
The recovery that had taken place during the years the exclusion zone was in place had been wiped out. ''It's back to how it was.''
Key dates in bid to impose temporary fishing closure on Astrolabe Reef
2015: Application lodged by Motiti Rohe Moana Trust
February 2016: Ministry calls for submissions
June 2017: Submitters notified of minister's decision.