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The Governor-General has received Scott Watson's petition to be pardoned and hopes to decide his fate within three months.

Watson, who was convicted of the murders of Ben Smart and Olivia Hope in 1998 and sentenced to a minimum non-parole period of 17 years in prison, wrote a 22-page letter late last year asking for a pardon or retrial in the Court of Appeal.

Ben and Olivia were last seen in the early hours of January 1, 1998 boarding a yacht in the Marlborough Sounds. Their bodies were never found.

After applications for retrials were denied by the Court of Appeal and the Privy Council, Watson was left with no choice but to claim a "miscarriage of justice occurred".

Watson's father Chris hopes Governor-General Anand Satyanand will issue a pardon. If that is unsuccessful the father and son want an independent inquiry.

"I suppose that's the only real way of addressing this situation ... an inquiry along the lines of the Arthur Allan Thomas case," Chris Watson said.

In Watson's application he wrote, "A miscarriage of justice occurred in [Crown] v Watson and this is now undeniable. I am innocent of the murders of Ben Smart and Olivia Hope and had no part in their disappearance."

A letter dated February 13 from the Ministry of Justice outlines the next stage of his petition for a royal prerogative of mercy, or pardon.

The letter says the "Minister of Justice will decide what advice to give the Governor-General".

The minister has the power to recommend three options; decline the application, refer the case back to the Court of Appeal, or grant a full pardon.

Ministry staff will review all the information sent by Watson.

It can then gather more information if needed to review the case.

"The ministry will aim to complete this initial planning stage within about three months of your response."

Chris Watson remains hopeful his son's life behind bars will come to an end but believes the ministry is "optimistic" thinking three months of work will do the case justice.