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The New Zealand Herald revealed in September that Justice Ian Binnie's report had concluded that, on the balance of probabilities, Mr Bain was innocent of murdering his parents, brother and two sisters in Dunedin in 1995, for which he served 13 years' imprisonment.
However, Justice Minister Judith Collins has rejected his report, saying it appeared to contain assumptions based on incorrect facts, and showed a misunderstanding of New Zealand law.
The report lacked a "robustness of reasoning used to justify its conclusions" and should be reviewed, she said.
From Geneva, Justice Binnie today released a statement from Geneva hitting back at her criticisms.
"The language of the press release shows it to be a political document which, given that the minister is engaged in a political exercise, is not surprising. "However I expected the minister to follow a fair and even handed process leading up to that political decision," he said.
In his statement, Justice Binnie also said it was unfair his report had not been shown to "the party most directly affected" - David Bain.
"The minister of course is free to seek advice wherever she wants but if she wanted input from the actual parties to the compensation inquiry (as distinguished from input from her colleagues or other persons with no axe to grind) she should surely have sought input from both sides. There may be much in my report that Mr Bain disagrees with. He doesn't know because he hasn't seen it."
New Zealanders had strong views about the David Bain case and most would want his compensation claim for wrongful conviction and imprisonment dealt with in an even-handed and fair way, said Justice Binnie.
In response to claims his report contained assumptions based on incorrect facts and a misunderstanding of New Zealand law, Justice Binnie said he received input from a "distinguished and totally independent New Zealand lawyer".
"Whatever else New Zealand law states, it is certainly well established that it is most improper for 'a client', especially a legally trained client, to attack publicly a lawyer's advice while simultaneously claiming privilege to protect from disclosure the advice that is being attacked. I would expect that the Minister, as a former Auckland tax lawyer, would be well aware of this principle."
Ms Collins said yesterday the report needed to be peer reviewed by New Zealand QC and former High Court Judge Robert Fisher.
She said she raised concerns directly with Justice Binnie at a meeting on September 13 at which Justice Secretary Andrew Bridgeman was present.
"I advised him I would be getting the matter peer reviewed."
Justice Binnie said he had no issue with his report being peer reviewed.
Mr Bain is asking the Ombudsman to intervene in his claim for compensation to direct Ms Collins to release the report to him.
Justice Binnie reportedly received $413,764 for his professional services and expenses.
Prime Minister John Key today acknowledged the costs associated with the process but it was "really important that we get it right so that is really a small price to pay," he said on TV3's Firstline.
Mr Bain's longtime advocate Joe Karam said the process was an "affront to natural justice".
He had spoken to Mr Bain last weekend and said he was "very, very upset".