Justice Minister Simon Power today announced retired Canadian Supreme Court justice Ian Binnie would hear the case.
"Due to the long-running and high-profile nature of the case, and after consultation with Mr Bain's lawyers, it was decided a judge from outside New Zealand would be appointed," Mr Power said.
"Justice Binnie's appointment is a significant step in attempting to resolve Mr Bain's claim for compensation and a step towards achieving finality in this case."
Justice Binnie, a Supreme Court judge for more than 13 years, was chosen from a list of several senior judges.
He was appointed a Queen's Counsel in Ontario in 1979 and was Canada's deputy justice minister from 1982 to 1986.
Canada has a similar compensation regime to New Zealand, Mr Power said.
Mr Bain's claim for compensation falls outside cabinet guidelines because he was acquitted following a retrial, but can still be heard due to the discretion to consider claims in extraordinary circumstances.
"The compensation framework requires claimants to prove their innocence, and at a minimum, under Cabinet guidelines, Mr Bain will need to establish his innocence on the balance of probabilities.
"But because his case falls outside the guidelines, something more is required that demonstrates that the circumstances are extraordinary, and Justice Binnie will decide the best process for assessing Mr Bain's claim against this test," Mr Power said.
Justice Binnie would begin work on the case before the end of the year.