The pair were arrested in Dubai in January 2009 based on subsequently discredited bribery allegations by Gold Coast property developer Sunland.
The charges were dismissed in the Victorian Supreme Court but the pair still face a lengthy prison term if a Dubai court finds them guilty.
Mr Fraser, a long-time friend of the Joyce family, says the men are innocent and has welcomed reports Britain's Prince Charles has become personally involved in the case.
But he also suggested Qantas had intervened to protect its partnership deal with Dubai's Emirates airline.
"Qantas would have been trying to get people to do nothing."
Qantas rejects the claim, saying it does not involve itself in legal matters regarding Australian citizens overseas.
"Any suggestion that we have encouraged a lack of intervention in a case involving Australians in Dubai is completely inaccurate," a spokesman said.
"That's completely wrong," Senator Carr's spokesman said, saying the government had raised it with Dubai dozens of times.
The case is to return to a Dubai court later this week.
The Australian newspaper says top barrister Jack Rush briefed Prince Charles' advisers on the case and the prince has since made behind-the-scenes representations to authorities in Dubai.
Sunland is appealing the Victorian judgment.