Rex Haig's bid for compensation after spending 10 years in jail has failed and the Queens Counsel looking at his case doubts his innocence.
Mr Haig has reacted angrily to the decision and he may appeal it.
Justice Minister Simon Power declined the compensation application on the advice of a report by Robert Fisher, QC.
Mr Haig served 10 years in prison after being convicted in 1995 for murdering Mark Roderique on his fishing boat off the West Coast.
He had said his nephew David Hogan, 31, one of the three crew members, was the murderer.
His conviction was quashed in 2006 by the Court of Appeal, after his lawyer presented affidavits from 14 witnesses saying Mr Hogan confessed or implicated himself in Mr Roderique's murder.
Mr Fisher's 189-page report detailed competing versions of what happened and the cover-up of the murder.
Both Mr Hogan and Mr Haig had motive and opportunity to kill Mr Roderique, he said.
Mr Haig was in financial difficulties, had tried paua poaching, and after a falling out with Mr Roderique was worried he would go to authorities.
Mr Fisher concluded that the men decided to kill Mr Roderique, dispose of his body and then cover it up.
He said Haig's book Rough Justice, the Rex Haig Story was "burdened by contrary evidence" and hundreds of witnesses conflicted with his account.
"I am satisfied that Mr Haig has failed to show that on the balance of probabilities he is innocent of the crime with which he was charged. If anything the inquiry suggests the reverse."
Mr Haig cannot be prosecuted again and Mr Fisher's findings relate only to the compensation decision.
Mr Fisher's investigation had to meet different criteria than criminal courts, which can only convict where there is proof beyond reasonable doubt, but in civil situations proof relies on the balance of probabilities.
When the Court of Appeal quashed Haig's conviction in August 2006 that was not a finding of innocence, Mr Fisher noted.
The judges said a jury might find Haig guilty only of being involved in the body's disposal and following cover-up. But they said a credible case remained and if there was a retrial it would be up to a jury to decide.
Mr Power said he found the report "clear, authoritative and persuasive," and so accepted its conclusion denying compensation.
Asked if he thought Mr Haig was guilty Mr Power said: "I've accepted the advice of the Queens Counsel."
Mr Haig said he should have got compensation but was unsurprised.
"The way the justice system works, they just want it to go away."
He said the report "raises more questions than it has answers" and his lawyer, Jonathan Eaton, had told him the lack of witnesses in the case made it difficult for a judgement on compensation to be made.
"But I consider the matter's unfinished because David Hogan should be arrested for this murder, because Robert Fisher has said that he has done the murder and there's a prima facie case against him for the murder of my witness, Anton Sherlock."
As part of Mr Haig's appeal, he claimed Mr Hogan contracted another man to murder his key defence witness, Mr Sherlock, in March 1995.
Mr Eaton said he and Mr Haig would consider the report before deciding further action.
A possibility was to challenge Mr Power's decision through a High Court judicial review.
Mr Eaton said it was virtually impossible for Mr Haig to "prove his innocence", which was the bar set for compensation.
He said Mr Fisher's rejection of Mr Hogan's original testimony - upon which Mr Haig was convicted - suggested police should reopen the case with a focus on Mr Hogan.
Since 1988 there have been six cases that reached the point where a QC considered compensation. Four were successful.
