A key piece of evidence used to make the decision was that the man's church attendance had dropped off in recent years.
However, the man may remain in Australia to appeal the decision on other grounds.
The man was challenging the fast-track visa process set up to clear the backlog of applicants, who arrived in Australia by boat between August 2012 and January 2014.
The man had arrived by boat, and argued he should not be sent back to Iran because he would be persecuted for converting to Christianity.
His case was reviewed by the Immigration Assessment Authority, which denied his application.
Key to the case was evidence from the man's church reverend, including a letter the man supplied confirming the fact he had attended the Melbourne church.
But in a follow-up phone call with the government delegate assessing the case, the reverend said the man had attended the church, but his attendance had dropped off significantly over the previous two years.
The reverend did note that the drop in attendance coincided with the man moving to another suburb.
The delegate later made the decision to deny the man a visa, on the grounds his conversion to Christianity was not genuine.
The man was never given details of the phone call, or given the chance to respond to them.
His lawyers from Victoria Legal Aid brought the case, arguing the man had been treated unfairly, because he was not given an opportunity to contest the information used to make the decision.
However, the High Court found the authority had exercised its discretion appropriately, and dismissed the man's appeal.
Chelsea Clark from Victoria Legal Aid's migration program said the fast-track review system remained an unfair process.
"The fast-track review system is a uniquely narrow method of government decision-making which is less fair, and less thorough, than the processes millions of Australians use each year to review government decisions that affect them," she said.
"In our client's case, the Court found that the delegate had not breached the legal obligations under s57 to provide our client with an opportunity to comment on adverse information."
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