The letter, sent to Peter Dutton two weeks ago, claims the Australian Federal Police knew the Bahraini red notice was invalid.
An international criminal justice watchdog has released a letter criticising the Australian government for facilitating the detainment of Bahraini refugee Hakeem Al-Araibi.
Mr Al-Araibi, an Australian permanent resident and semi-professional football player, is facing deportation to Bahrain after he was arrested on an Interpol red notice when he arrived in Bangkok with his wife in late November.
In the letter, addressed to Home Affairs Minister Peter Dutton and dated December 12, Fair Trials accused the Australian Federal Police (AFP) of being aware of Interpol's refugee policy which states that red notices are not allowed against refugees and asylum seekers if the alert was requested by the country where they fear persecution.
"No doubt the AFP, acting as Australia's National Centre Bureau for Interpol, should have been aware of this policy, and if it knew about Mr Al-Araibi's refugee status, then it must have also known that the Bahraini Red Notice against him was invalid," the letter read.
"Any attempt by the AFP to justify its actions on the basis that it was acting in good faith to facilitate police cooperation is indefensible."
Mr Al-Araibi's visa allows him to remain in Australia indefinitely and to travel to and from the country as long as he does not return to his homeland.
But it has been revealed that Australia's National Interpol Bureau tipped of Thailand prior to Mr Al-Araibi's arrival.
Thailand would be in breach of international law if it proceeds with his extradition.
The Bahraini government alleges the footballer "deliberately attacked a police station with improvised explosive devices" in 2012, however, a video has been published by the Bahrain Institute for Rights and Democracy reportedly to show Mr Al-Araibi playing in a live football match at the time of the incident.
"Fair Trials appreciates that there is a pressing need for effective cross-border police cooperation, but this has to be subject to safeguards that prevent human rights abuses like the ones that Mr Al-Araibi is currently facing," the Fair Trials letter reads.
"This is precisely why Interpol itself has rules that aim to respect human rights and prevent the use of politically motivated alerts. It is crucial that Australia takes the same approach.
"We believe that the first step that the Department of Home Affairs should take to prevent cases like Mr Al-Araibi's from happening in the future is to acknowledge that there is room for improvement - not to defend the clearly unjustified actions and pass the blame on to other countries."
"It is a tragic case and we need to do as much as we can as a football community to bring it back home," Football Victoria chief executive Peter Filopoulos said in a video posted on social media.
"Bring him back to Victoria, Australia so he can resume the life he has chosen to live here in Australia, where he plays in for one our second-tier clubs in the National Premier League in Pascoe Vale."
The world football governing body FIFA has also pushed for the footballer's release.
At the time of writing, a GoFundMe aiming to raise enough money to provide Mr Hakeem with a human rights lawyer in Thailand has reached $4522.
Fair Trials is an international group of legal experts based in London, Brussels and Washington, DC.