More than 100,000 Afghan nationals are seeking humanitarian visas from Australia, officials have revealed, with demand far outstripping the 3,000 places the federal government initially allocated when Afghanistan fell to the Taliban.

Officials have also revealed nearly 300 Australian citizens or permanent residents remain in Afghanistan, with an unspecified number of those seeking help from the government to leave the country.

On Monday, humanitarian advocates told a Senate inquiry Afghans were living in “fear and uncertainty”. In recent days, a witness told the hearing, the Taliban had attacked a former security guard who had helped Australia and been left behind in the August evacuation mission.

Confirming the scale of the crisis, the Department of Home Affairs said Australia had received 26,000 applications from Afghan nationals for protection in the past seven weeks.

Given that these applications often include family groups, officials estimated that meant more than 100,000 people were seeking help from Australia.

David Wilden, a first assistant secretary at the Department of Home Affairs, said applications had spiked after the fall of Kabul and the government had received them “in very large volumes daily ever since then”.

Australia was still going through those applications, but they may include people still in Afghanistan and people outside of the country, and some with and some without connections to Australia, he said.

Wilden said while the government had allocated 3,000 places within the existing humanitarian program this financial year, this was “the floor”, not the ceiling on Australia’s intake. He said it was open to the government to take a higher number.

Australia’s current annual humanitarian intake, from all countries, is 13,750 people – a number that was lowered by the Coalition. The Refugee Council of Australia is among groups calling for a special intake of 20,000 places for refugees from Afghanistan.

Sitarah Mohammadi, of the Afghanistan-Australian Advocacy Network, urged the Australian government on Monday to announce a special humanitarian intake targeting particularly at-risk groups.

She told the inquiry the people of Afghanistan were now living under “fear and uncertainty” under Taliban rule. Mohammadi said the Taliban was “brutal and ruthless” and the future “looks grim” for women and girls.

Atika Hussain, a lawyer and member of Australia’s Hazara diaspora, said in a statement it was “morally wrong to leave vulnerable religious minority groups such as Hazara at the mercy of the Taliban who have been perpetrators of hideous attacks against the group”.

Hussain said Australian Hazaras had had family members killed in the Taliban attack on Ghazni in June this year, while others have had family forcibly displaced by Taliban attacks on Daikundi.

“It is disturbing to learn that each terrorist attack in Afghanistan leaves victims in Australia from the Hazara community,” Hussain said. “Therefore, we are calling for an increase and prioritisation of the humanitarian intake for most persecuted groups such as Hazara.”

At the Senate inquiry, Kay Danes, a humanitarian advocate with GAP Veterans and Legal Services, said security guards who had helped Australia and remained in Afghanistan were now hiding in safe houses.

“We had one guard only a day or two ago beaten up by Taliban,” Danes said. “His mother, thank God, saved him, bless her. She was hanging on to him and wouldn’t let them take him away from the house.”

Australian officials defended the military-led mission that airlifted 4,100 people out of Kabul in August – and the lack of an earlier evacuation operation.

Simon Newnham, an acting deputy secretary at the Department of Foreign Affairs and Trade, said the evacuation flights were arranged “amidst the most challenging of circumstances”. He said two-thirds of the evacuees were women and children.

Newnham acknowledged the “desperate circumstances” of those who went to the airport in Kabul, as they suffered crushing crowds, violence and the “depraved terrorist attack of 26 August as the evacuation window closed”.

Daniel Sloper, the Australian government’s special representative on Afghanistan, joined the hearing from Doha. Reflecting on the August evacuation mission, he said bluntly: “We’re very conscious we left behind others.”

Sloper said he was not engaging directly with the Taliban “at this point”, although some close partners of Australia were engaged on practical issues.

Home affairs officials gave a breakdown of the number of applications received under the locally engaged employees program in the months leading to the Taliban’s full takeover of Afghanistan.

They received five new applications in April, covering 23 people when family members are included. That was followed by 13 applications (62 people) in May, 14 applications (62 people) in June, and 11 applications (50 people) in July.

The number of new applications from former locally engaged employees spiked to 68 (293 people) in August, the month the Taliban seized Kabul.

The chief of the ADF, General Angus Campbell, was asked about the government publicly ruling out a military-run evacuation mission in July, with the emphasis then being on commercial flights.

Campbell noted it was “a matter for government” to decide, but added: “In July there was no military reason for an evacuation operation to be conducted by the ADF.”

Campbell said demand for the locally engaged employee program increased from early August amid a “very dramatic taking over of a whole series of provincial capitals” by the Taliban.

Hugh Jeffrey, a senior defence department official, said: “It is true that the [then] Afghan government was sensitive to the idea or the image of countries departing Afghanistan quickly or in haste.”

The Australian government closed its embassy in Kabul in May based on advice about the deteriorating security situation.

Campbell said he was “very alive” to the “worst case” future scenario of having to rescue officials from the embassy at the same time as rescuing locally engaged employees and Australian citizens, permanent residents and visa holders.

Defence advised the government “that the embassy ought withdraw when Australian forces are withdrawing, because that gives us confidence that we would not have an embassy team, isolated in extremis, if the worst were to happen”.

Additional reporting by Ben Doherty