Late last year, Michael Daniel Thompson and Able Seaman Rohan Martin Angre pleaded guilty to charges of forcible confinement, committing an act of indecency and assault occasioning actual bodily harm over an incident on board the guided missile frigate HMAS Newcastle in August 2011.

At a court martial in Sydney, prosecutors alleged Mr Thompson and Able Seaman Angre were among a group of sailors who hog-tied and assaulted a young colleague during a last night at sea ritual off the West Australian coast.

The sailor was allegedly stripped, wrestled to the ground and tied with cable ties as a crowd of other sailors looked on.

His buttocks were allegedly smeared with a substance alleged to be a mix of Vegemite and Deep Heat, and a rubber chicken was inserted into his anus.

He was then allegedly carried into the shower and doused with a dark liquid causing painful skin and eye irritation.

Able Seaman Angre and Mr Thompson pleaded guilty in exchange for an agreement by the prosecution to drop the rape charges, not to seek a sentence of imprisonment, and for the matter to be dealt with by a Defence Force magistrate rather than a general court martial.

This would have dramatically reduced the likelihood of either man going to jail.

But the prosecution and the defence did not realise that, under the Defence Force Discipline Act, a new court martial had to be convened after a conviction was recorded.

Mr Thompson, who now has a new lawyer, appealed against his conviction to the Defence Force Discipline Appeal Tribunal, which found that the errors amounted to a "substantial miscarriage of justice" and ordered a retrial.

"I would not have changed my plea to guilty and endorsed the agreed statement of facts had I not been wrongly advised about being sentenced by a Defence Force magistrate," Mr Thompson said on Sunday.

"I was enticed into taking that deal with them, when the prosecution should have known that they couldn't live up to their end of the bargain."

Able Seaman Angre, who also has a new lawyer, was seeking to withdraw his guilty plea to the charges.

He was claiming not only to have suffered the same miscarriage of justice as Mr Thompson, but that he was a victim of alleged impropriety by investigators from the Australian Defence Force Investigation Service.

In his written application, which has been widely circulated in defence legal circles, Able Seaman Angre said investigators were "allegedly involved in the manufacture and manipulation of evidence during the investigation of the allegations which they provided to the prosecution to adduce at the trial".

He also asserted he was under pressure from his defence lawyer to plead guilty, and that the Judge Advocate did not ensure he fully understood the implications of the plea.

The Australian Defence Force said it was unable to comment because they were "currently a part of legal proceedings".

The application will come before the Chief Judge Advocate on June 17.