Refugee advocates are pleading with the Australian government to reconsider deporting a young Tamil man who says he could face torture, interrogation or death if he is sent back to Sri Lanka.

The man, known only as Rajah, arrived in Australia by boat after fleeing persecution in Sri Lanka in 2012, according to Refugee Advice and Casework Service (RACS) lawyer Sarah Dale.

Rajah, who is expected to be deported on Wednesday night, missed the October 1 deadline to file for refugee status and was moved from his western Sydney home to the Villawood detention facility.

Dale said Home Affairs Minister Peter Dutton has the power to review the man's application and keep him in Australia.

"He fears for his life, he fears interrogation, he fears significant harm returning to Sri Lanka," Dale told AAP at Sydney Airport just hours before her client is scheduled to be deported.

"He is petrified of what he's going to return home to."

RACS executive director Tanya Jackson-Vaughn described the handling of Rajah's case as an "extraordinary injustice".

"People who come seeking asylum to Australia have the right to claim protection," Ms Jackson-Vaughn told AAP.

"I feel that it's an extraordinary injustice that his claims haven't been assessed and that he's been thrown on a plane and deported back to where he fled from."

Both Dutton and the Immigration and Border Protection Department have been contacted for comment.