The impoverished Philippine and Sri Lankan refugees helped the former National Security Agency contractor evade authorities in 2013 by hiding him in their cramped homes after he initiated one of the largest data leaks in US history.
They have spent years hoping the Hong Kong government would recognise their cases and save them from being sent back to their home countries where they say they were persecuted.
They now face deportation.
"These are good people that were driven from their homes by torture, rape, abuse, blackmail and war, circumstances that are really difficult for us to imagine," Snowden said in a video released today.
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"Now what they're facing is a transparent injustice from the very people that they asked to protect them," he said.
He has been living in exile in Russia since the summer of 2013. Russia's immigration service in January extended Snowden's residency permit to 2020.
After leaving his initial Hong Kong hotel bolthole for fear of being discovered, he went underground, fed and looked after by the refugees for around two weeks.
Their stories only emerged late last year.
The refugees' lawyer, Robert Tibbo has called the decision by Hong Kong authorities "completely unreasonable", and said he had less than two weeks to submit appeals before the families were deported.
Hong Kong is not a signatory to the UN's refugee convention and does not grant asylum.
However, it is bound by the UN Convention against Torture and Other Cruel, Inhuman or Degrading Treatment or Punishment (UNCAT) and considers claims for protection based on those grounds.
One of the refugees, Vanessa Rodel from the Philippines, who lives in Hong Kong with her five-year-old daughter, broke down over the news of the decision.
Another of the refugees, Ajith Pushpakumara from Sri Lanka, told AFP the government had "taken his whole life".