"The commission's actions were, therefore, not in breach of natural justice.''
The applicants said the late evidence from the witnesses which gave them no opportunity to cross-examine them was a "breach of natural justice''.
However, Justice Young said the applicants accepted that the evidence of the witnesses did not cover new topics or new matters.
"The evidence was `new' only in the sense that these three witnesses had not previously given this evidence directly to the commission. Thus the commission already had evidence on the issues raised in the three witnesses' evidence.''
He said the applicants were aware of all evidence filed with the commission after it finished on April 4.
They were also provided with an opportunity to respond to that evidence, he said.
Justice Young also ruled that the release of the commission's report would not unfairly prejudice any future trials.
Whittall and Pike River Coal face a total of 21 charges, brought by the Department of Labour relating to a series of explosions in the mine that killed 29 workers in November, 2010.
The maximum penalty for the offences Whittall faces is a fine. He has indicated he will plead not guilty and any trial will be before a judge alone.
The trial was unlikely to begin earlier than 12 to 18 months from the release of the commission's report into the mine's explosions, Justice Young said.
Grey District Mayor Tony Kokshoorn welcomed the decision.
"The people of the West Coast have had a gutsful of the mitigation and the stalling that (Peter) Whittall and his lawyers are putting up.
"We just want this to move on now.''
Mr Kokshoorn said the community had heard ``word for word'' everything that was said during the commission hearings and they had made their own decisions on who was to blame for the tragedy.
"We just want now the commission to confirm what we're all thinking.''
He said the commission had done a thorough job and they had all the information they needed to make the best decision.
"You can't bring the men back but at least we can go into the future probably with safer mines as a consequence and that's what those men would like as their legacy.''
Bernie Monk, spokesman for the families of the men who died, said Justice Young's decision was expected.
"A lot of the information that they were going on about was already in the commission.''
The commission had given the applicants many opportunities to question the evidence, he said.
"I think they've been over fair on what they've done. So it was totally expected from my point of view and as it turns out they've made the right decision.''
He said the other family members would also welcome the result.
Whittall was not immediately available for comment.