The Australian Border Force has confirmed that an asylum seeker has died by setting fire to himself while living in the community on a bridging visa.

On Monday, Guardian Australia revealed that asylum seeker Khodayar Amini, a Hazara Afghan terrified of being sent back to detention, set fire to himself while on a video call to refugee advocates at the weekend.

During a Senate estimates hearing in Canberra on Monday night, Greens Senator Sarah Hanson-Young questioned officials from the Australian Border Force and the immigration department about the death.

Mike Pezzullo, the secretary of the Department of Immigration and Border Protection, said he had received “operational reports of a person, who is not in detention, self-harming in that way”.

Hanson-Young asked: “So has that person died?”

Outram replied: “We understand that there is a death of somebody who was in the community, someone who was known to the department”.

On Monday afternoon, Guardian Australia asked both departments whether there had been plans to return Amini to detention before his death, or to send him back to Afghanistan, where most of his family had been killed by the Taliban. Amini has no known family members in Australia and was believed to have been living out of his car in Victorian bushland when he died.

Hanson-Young again asked those questions during the hearing, and was told they would be taken on notice.

Michael Outram, the assistant commissioner of the Border Force, said a coronial inquest was needed to confirm the circumstances of the death of the man, who was yet to be formally identified as Amini.

On Tuesday, Hanson-Young said she was disappointed that department staff had so far been unable to give clarity to the man’s situation and visa status.

“There needs to be a full, independent investigation into this case so that we can understand why this young man didn’t receive the support that he so clearly needed,” she said.

“As a nation, we need to think long and hard about how we treat people who have come to Australia seeking safety.”

NSW police later confirmed to Guardian Australia that on 21 August a 30-year-old man was charged with using a carriage service–- a phone, email, or other form of electronic communication – to threaten to kill, stalk, or intimidate.

The charges, laid by officers from Flemington local area command, relate to “an alleged offensive and threatening phone call received by an organisation”, a police spokeswoman said.

Amini had been scheduled to appear in Burwood local court on 10 November.

Asylum seekers on bridging visas are obliged to sign a stringent “code of behaviour”, which includes a clause relating to obeying all Australian laws. Asylum seekers who breach the code can have their visas summarily cancelled, and be removed from the country.

Guardian Australia understands immigration department officials wanted to interview Amini in relation to those charges, and his alleged breach of the code.

At about 11.30am on Sunday, Amini made a video call to advocates from the Refugee Rights Action Network in Western Australia and told them he feared he would be returned to detention because police and immigration department staff wanted to interview him.

He then self-immolated in front of the advocates, Sarah Ross and Michelle Bui.

Guardian Australia has seen messages sent by Amini, aged 30, to the advocates in the weeks leading up to the incident, in which he spoke of his distress that several of his asylum-seeker friends had taken their own lives or died while in detention.

By the time he called the advocates on Sunday, he was “inconsolable”, Bui said.

“Unfortunately, our efforts to console and calm him were vastly inadequate when set against the fear and desperation provoked by the prospect of being re-detained and dying in a detention centre,” she said.

“I think for all those living in limbo, on bridging visas in the community, the threat of re-detainment is omnipresent. This is yet another signal for the need to end mandatory detention and provide people with a fair and just processing system, that doesn’t leave them waiting in uncertainty for years on end.”

Violence against Hazaras is escalating in Afghanistan, where they are an ethnic minority.

Cindy Briscoe, deputy commissioner in the ABF support group, said between January 15 and August 15, there were 74 self-harm incidents and 23 threats of self-harm at the Nauru offshore processing centre. In the same period, there were 34 cases of self-harm and two threats of self-harm at the Manus Island processing centre, she told the estimates hearing.