Saffrine Duggan said her husband Daniel Duggan had already been kept 115 days in a "tiny cell" in Sydney's Silverwater prison based on US charges that had yet to be tested in court.
"He is suffering the harshest possible prison classification in Australia as an 'extreme high risk restricted inmate' despite having no prior (or current) convictions," she said in a statement.
"This is unprecedented and an affront to Australia's rule of law and manipulation of the Australian legal system by the United States, at the expense of the Australian taxpayer."
Already filing a complaint with the Inspector-General of Intelligence and Security, Mrs Duggan said a further complaint would be filed with the United Nations Human Rights Committee.
"The manner and circumstances behind this prosecution of Dan are something you would expect to find in an authoritarian country, but not in a democratic Australia where its citizens expect a more fair and balanced equal application of the law and the overriding principle of a 'fair go' for all," she said.
Duggan, 54, was arrested in October last year near his family home in Orange, central west NSW, and accused of providing military training to pilots working for China.
He has denied the allegations brought against him, saying they were "political" posturing by the US which unfairly singled him out.
Mrs Duggan said the treaty under which the FBI had attempted to extradite her husband was not being used properly.
"The treaty specifically states that alleged crimes under its provisions should not be of a 'political character', should require dual criminality - which is not the case in this instance - and should be in Australia's national interests," she said.
The case is proceeding through the Local Courts where a magistrate will decide whether Duggan is eligible for extradition. It will then be up to Attorney-General Mark Dreyfus to make the final call.
Born in Boston, Duggan served in the US Marines for 12 years before immigrating to Australia in 2002. In January 2012, he gained Australian citizenship, choosing to give up his US citizenship in the process.
The matter will next come before Downing Centre Local Court on March 20.
