In the Federal Circuit Court yesterday, Judge Nicholas Manousaridis dismissed an application by the man to halt his deportation.

"Please help me," the man, speaking Hazaragi, told the court through an interpreter.

Previous forcible deportations have seen Hazaras returned to Pakistan, but never to Afghanistan.

The 29-year-old ethnic Hazara, known to the court as SZUYW, first fled Afghanistan for Iran. Iran systematically deports Afghan asylum seekers and, having been ejected, the man then came to Australia by boat, arriving in December 2011.

His claim for asylum was rejected, and his appeal to the Refugee Review Tribunal in December 2012 failed, the tribunal ruling that it was safe to live in his home district of Jaghori, in central Afghanistan, which is majority Hazara.

"The Tribunal notes that there is a significant population living in Jaghori. His family are living there … [and] as there is a route from Kabul to Jaghori that is secure, there is not a real risk the applicant will suffer significant harm."

The man told the court yesterday he feared the Taliban.

"Jaghori is confined, it's like a prison, the surrounding areas are all controlled by the Taliban. Many people die on the way to Jaghori."

The Taliban have made significant advances in recent months, and now control several highways surrounding Kabul, including the so-called "Death Road" to central Afghanistan, which is rarely travelled now after dozens of beheadings, kidnappings and bombings.

Ian Rintoul, from the Refugee Action Coalition, said the Refugee Review Tribunal's security assessment was based on information now more than two years old. More recent RRT decisions have ruled Jaghori district was not a safe place for Hazaras to return to.

"It makes no sense to send someone back to a country that is descending into war, which Afghanistan is. The security situation has deteriorated dramatically and will only get worse. Hazaras are being targeted by the Taliban."

The United Nations General Assembly report on Afghanistan, from March this year, found the security situation "remained volatile" and that armed clashes had increased 51 per cent since 2012.

Australia has returned refugees to Afghanistan before, but never against their will. In 2001, 179 refugees from the MV Tampa were returned to Afghanistan, after agreeing to go back while being held on Nauru.

An investigation by Fairfax Media in 2011 found at least 20 returned refugees had been killed in their homeland, several had fled again, for Australia and other countries, while more than a dozen remained in hiding.

The Refugees Convention, to which Australia is a party, prohibits refoulement, sending refugees back to a place where their "life or freedom would be threatened".

The man was taken from Villawood detention centre where he was being held, and left Australia on a 9:40pm flight.