"There is undoubtedly a level of unfairness created here," the judge said in his decision.
The helicopter operators were consulted on the changes but recreational hunters were not.
"Consideration also needed to be given to affording a similar opportunity to the recreational hunters who would be most affected by any changes," the judge said.
"I am satisfied this has been an unfair process caused by a failure to consult with the applicant."
The judge ruled the decision "was invalid due to a failure of natural justice."
He did not, however, quash the concessions made to helicopter hunters following the 2015 decision.
He awarded court costs to the hunters, but no monetary award or immediate alteration of the decision.
Lower North Island Red Deer Foundation president Gordon George said the Department of Conservation had wasted time and money by insisting the matter go to court.
"The whole process has been time-consuming and costly and DoC has wasted taxpayer dollars," George said.
"In the end we had no choice but to go to court ... we hope the department will now start consulting properly with recreational hunters as it is required to do."
A spokesman for the Department of Conservation, Jay Eden, said DoC was "still considering" whether to appeal the decision.
"While the Court was clear DoC should have consulted LNI recreational hunters in this case, no other relief was ordered.
"The High Court decision does provide guidance for DoC on how to undertake the next WARO permit round, which DoC will consider."