An Australian former Catholic school teacher will face trial on pedophile charges next week after an appeals court in Phnom Penh rejected two annulment attempts, deigning one was outside the court's jurisdiction and in the second he had no right to question police interviews, his lawyer says.

Mulroy, from Lismore in northern New South Wales, was not allowed to attend Tuesday's closed hearing and instead awaited the decision from his prison cell in the northwest city of Siem Reap.

His lawyer So Mosseny said he was disappointed by the decisions, adding there was no right of appeal for annulment.

"They rejected it, I didn't think that's a fair decision," he said. "You can not appeal, there are no checks and balances."

The Investigative Chambers of the Phnom Penh Appeals Court ruled on two submissions. The first was to annul the charges amid defence claims of a lack of police evidence. The second was made on the police evidence itself and follow-up interviews with witnesses, arguing it was coerced.

Mulroy's case won the attention of Australian Prime Minister Scott Morrison after an independent report commissioned by the defence found no evidence to support the charges and that Mulroy was the victim of an extortion bid amid petty rivalries among foreign-run charities.

The prosecution says the 64-year-old had attempted to establish an NGO called Education House with six children who police later alleged he had procured for sex in exchange for food and money.

However, the report, by risk management consultant Ross Milosevic, including affidavits from people who knew the children, found no evidence to support the charges and that police interviews were made "under extreme duress, intimidation and extortion".

"I can honestly say these boys were never abused by the accused. The boys' honesty and demeanour showed no attitude that they were ever mistreated or abused sexually in anyway," the report cited a witness, whose name has not been released, as saying.

Speaking outside the court recently, Mulroy told AAP: "I am innocent, yes.... What irks me is the boys, they have lost an opportunity for an education and life in general."