Key Points:

Scott Watson has broken an 11-year silence from jail to explain his claim that he is innocent of murdering Ben Smart and Olivia Hope in 1998.

Serving life in prison with a minimum non-parole period of 17 years, Watson has written a 22-page letter to the Governor-General, who can recommend he be pardoned or refer the case back to the Court of Appeal.

The Court of Appeal dismissed an application for a retrial on points of law in 2000, as did the Privy Council, but Watson said the case against him had "dissolved" and no longer existed.

"A miscarriage of justice occurred in R v Watson and this is now undeniable," Watson wrote. "I am innocent of the murders of Ben Smart and Olivia Hope and had no part in their disappearance."

As part of his petition to Governor-General Anand Satyanand, Watson enclosed a copy of Auckland journalist Keith Hunter's book Trial by Trickery and award-winning documentary Murder on the Blade?

Hunter makes serious allegations against the police investigation, which are under investigation by the Independent Police Complaints Authority.

High-profile defence lawyer Greg King said the jury accepted the evidence at the original trial, but new evidence produced since was the key to overturning Watson's convictions.

Ben and Olivia were last seen boarding a yacht moored off Furneaux Lodge in the Marlborough Sounds in the early hours of January 1, 1998.

In his letter Watson said a new jury would hear that:

Key police witnesses Guy Wallace and Roz McNeilly have recanted their evidence of picking Watson from a photo montage.

A secret witness has recanted his evidence that Watson confessed to him while in jail.

Sailing speed tests show it was impossible for Watson to have been seen in the Cook Strait when police say he was.

There was no evidence to prove Watson made two trips to shore on the night Ben and Olivia disappeared, a theory the Crown revealed on the last day of a 13-week trial.

There were dozens of sightings of a two-masted ketch which Wallace was adamant he took Ben and Olivia to but which police say did not exist.

The head of Operation Tam, Detective Inspector Rob Pope _ now the Deputy Police Commissioner _ would be called to give evidence if a retrial was ordered, wrote Watson.

He asked the Governor-General to pardon him under the royal prerogative, on advice from the Ministry of Justice, or for the case to be reheard at the Court of Appeal.

He also asked that an independent inquiry be held into the police investigation of the murders, the "trial by media" and subsequent prosecution.

King said a full Ministry of Justice investigation with wide powers, similar to inquiries into the convictions of Peter Ellis and Rex Haig, was needed to explore the "myriad of issues" in the Watson case.

"We've put the ball in their [Ministry of Justice] court because this is the only way forward," said King.

"A verdict from a jury confronted with this new evidence would look a bloody sight different than [one] from 1998. It's not a safe conviction."

Since November last year, Pope has declined to be interviewed after coverage in the Herald on Sunday and North & South magazine, which raised serious questions about the case.

Even Olivia Hope's father has expressed growing doubt about Watson's conviction.

"What we got was a conviction but we never got the truth," said Gerald Hope. "And that's the part that still really rips me up.

"I'm not saying [Scott Watson] is not guilty. What I'm saying is let's clear up the doubt."

Hope said he was amazed that nobody _ especially politicians _ had responded to Hunter's stinging attack in Trial by Trickery on those who put Watson away.

Meanwhile, a police inquiry into allegations that Pope swore misleading affidavits during the investigation has still not been released.

Watson's father, Chris, laid the complaint in 2004 but it was not acted on until Act Party leader Rodney Hide and the Herald on Sunday questioned Police Minister Annette King in March.

Police spokesman Jon Neilson said an independent lawyer had reviewed the report by Detective Inspector Ross Pinkham in April and "a couple of matters" were expected to be resolved shortly.

A separate Independent Police Complaints Authority inquiry into the same allegations is also under way.