A Royal pardon for Harry "Breaker" Morant has been refused in a modern-day appeal that is as mysterious as the century-old case that saw the Australian soldier executed.

Morant's death by firing squad in 1902 was one of the most controversial events in Australia's military history.

He, along with two other Australian soldiers, were accused of murdering prisoners during the Boer War. Peter Handcock was executed with Morant, but the third man was acquitted of the murders after serving several years jail.

It has long been argued the men were following orders from their British superiors or were not involved in the killings at all.

Late last month the British government said there was no new evidence to take the case forward after Australian military lawyer Commander James Unkles petitioned the Queen for a Royal pardon for Morant and Handcock.

Commander Unkles says much like the original trial, this latest review of the case - led by British defence secretary Liam Fox - was shrouded in secrecy.

"This case seems to have a history from its very inception of running in secret and without involvement or exposure to the public and that's how the trials were conducted in 1902," he said.

"The internal processes and workings of the British government seem to be replicating what happened 108 years ago."

Commander Unkles is convinced the British government is hiding something.

"I've examined the written notice that [UK defence secretary Liam Fox] has given the Australian Attorney-General and I still think the British are hiding something," he said.

"They don't want to bring this case out into the public.

"The case has been examined behind closed doors by public servants, lawyers and historians who have advised the minister that the conviction should stand, that there's nothing compelling, nothing new."

Call for inquiry

Commander Unkles has spent one-and-a-half years working on gaining a pardon for Morant - the legendary horseman, bush poet and rumoured womaniser, who signed up to help the motherland in the Boer War.

Commander Unkles was researching Morant's lawyer Major James Thomas when he became convinced the soldiers were innocent.

"It became very apparent to me that a major injustice had been committed and the only way it was going to be addressed was by taking some action," he said.

As with most controversies, this one is mysterious. Commander Unkles says many transcripts from the original trial are missing and there are all sorts of theories as to their whereabouts.

But he says he has enough evidence to prove the Australians were not guilty of murder.

Commander Unkles is calling for a judicial inquiry into the original trial.

"I think the only way the controversy behind this case will ever be settled is through the appointment of a judicial inquiry, a senior judge to assess and investigate all the claims and counter claims of this case," he said.

Commander Unkles says the families of Breaker Morant and the other Australians have had to live with their sentences and this is a chance for them and Australia to correct history.

"I seek to represent the interests of the descendants of these men who have had to struggle with this case over many decades in their family histories," he said.

He says he believes a judicial inquiry would find the British military made serious errors and the three inexperienced Australian volunteers were not at fault.