The Rebels announced on social media they had secured a new commercial partnership with Thai Airways, a company whose government is the majority shareholder.
The Twitter post prompted major backlash led by former Australian soccer captain Craig Foster, coming a day after Australian refugee and soccer player Hakeem Al-Araibi appeared shackled in a Bangkok court.
Al-Araibi is being held in a Thai prison as he fights extradition to his former homeland, Bahrain, where he fears he will be tortured.
"Guys, seriously. A fellow Australian is in shackles. And an athlete #SaveHakeem", Foster tweeted.
Following a flood of criticism, the Rebels issued an apology tweet explaining the deal was not an "endorsement for the breach of any individual's rights" and pledging to use their new relationship to help Al-Araibi's situation.
"We have not meant to cause any offense with this announcement and apologise unreservedly if it has done so," the Rebels statement read.
"This commercial relationship with an airline is in no way intended to be an endorsement for the breach of any individual's rights or the actions of any government.
"We support the movement to #SaveHakeem and will use our new relationship with the airline to engage with them directly."
Despite the apology the Rebels plan to keep the new deal.
Football Federation Australia on Wednesday cancelled a scheduled Olyroos camp in Thailand, with the federal government also condemning Thailand's handling of Al-Araibi.