A senior Taliban commander met a former Afghan president, Hamid Karzai, for talks on Wednesday, as the Taliban worked to establish a government in Afghanistan amid allegations of women and children being beaten and at least three protesters being shot dead.

Karzai, president from December 2001 to September 2014, has been leading efforts to ensure there is a peaceful transfer of power after Kabul fell on Sunday and the president, Ashraf Ghani, fled while the Taliban declared themselves the victorious rulers of Afghanistan.

Ghani’s whereabouts have been the source of much speculation, but a statement by the United Arab Emirates foreign ministry confirmed that he and his family had been welcomed into the UAE “on humanitarian grounds”.

Late on Wednesday, the former president said that he hoped to return home, and expressed support for talks between the Taliban and top former officials.

“For now, I am in the Emirates so that bloodshed and chaos is stopped,” he said in a video message – his first appearance since leaving the capital on Sunday. He said he had “no intention” to remain in exile. “I am currently in talks to return to Afghanistan,” he said.

Many Afghans consider Ghani to have betrayed his country, and the Afghan embassy in Tajikistan called for an Interpol arrest warrant to be issued for him on the grounds of “treasury theft”.

Asked for a US reaction to Ghani’s flight to the UAE, the deputy secretary of state, Wendy Sherman, was succinct and pointed. “He is no longer a figure in Afghanistan,” she said.

Joe Biden defended the rapid US troop withdrawal which opened the door to the Taliban’s lightning offensive and the collapse of the Afghan government, saying he could not see a way to withdraw from Afghanistan without “chaos ensuing”.

Asked by ABC News’ George Stephanopoulos if the US exit could have been handled better, the president said: “The idea that, somehow, there’s a way to have gotten out without chaos ensuing, I don’t know how that happens.”

The Taliban have been forceful in their efforts to portray themselves as the civilised new leaders of Afghanistan, saying they sought to form an “inclusive, Islamic” government. They declared an “amnesty” for government workers, and officials were told to return to work as normal. “We want to make sure that Afghanistan is not a battlefield of conflict any more,” Zabihullah Mujahid, a Taliban spokesperson, told a press conference on Tuesday.

But their talk of moderation and peace was punctured by allegations of women and children being beaten and whipped by Taliban fighters as they tried to reach Kabul airport, protesters in several cities being beaten and shot dead, and the statue of an enemy figure being blown up.

The meeting on Wednesday was between Karzai and Anas Haqqani, senior leader of the Haqqani Network militant group, an important faction of the Taliban. The previous government’s main peace envoy, Abdullah Abdullah, was also present.

The US has classed the Haqqani Network, based in the border regions with Pakistan, as a terrorist network, holding it responsible for some of the most deadly militant attacks in Afghanistan in recent years. The group’s involvement in a future Taliban government is likely to be problematic for the international community.

A spokesperson for Karzai said the meeting’s aim was to facilitate negotiations with Mullah Abdul Ghani Baradar, the influential Taliban political leader who led the agreement for the withdrawal of US troops and is believed to be taking an important role in the government. Baradar returned to Afghanistan on Tuesday for the first time in 20 years.

Waheedullah Hashimi, a spokesperson for the Taliban, told Reuters that the country was likely to be governed by a ruling Taliban council, while the Islamist militant movement’s supreme leader, Haibatullah Akhundzada, was expected to remain in overall charge, in a role akin to the president.

The power structure that Hashimi outlined would bear similarities to how Afghanistan was run the last time the Taliban were in power from 1996 to 2001. Then, supreme leader Mullah Omar remained in the shadows and left the day-to-day running of the country to a council.

Taliban leadership will meet later this week to discuss and set out the system of governance, but any semblance of democracy has already been ruled out.

“There will be no democratic system at all because it does not have any base in our country,” Hashimi said in an interview with Reuters. “We will not discuss what type of political system should we apply in Afghanistan because it is clear. It is sharia law and that is it.”

Hashimi said Taliban would also ask former pilots and soldiers from the Afghan armed forces to join its ranks. He did not allay fears that this Taliban regime would be as repressive towards women as it was last time they were in power.

“Our ulema [scholars] will decide whether girls are allowed to go to school or not,” he said. “They will decide whether they should wear hijab, burqa, or only [a] veil plus abaya or something, or not. That is up to them.”

After president Ghani’s escape on Sunday, one of the few figures from the previous regime still publicly resisting Taliban rule was the former vice-president, Amrullah Saleh, who declared himself the rightful caretaker president. Saleh, who is believed to be in hiding in Panjshir valley, north of Kabul, one of the few districts that has not fallen to insurgents, said on Twitter that he would “under no circumstances bow” to “the Talib terrorists”.

He received online promises of support from accounts that said they belonged to government soldiers, along with posts saying troops loyal to the memory of Ahmad Shah Massoud, the leader of the Northern Alliance assassinated by two al-Qaida operatives just before the 9/11 attacks on the US, were converging on Panjshir to form a “Resistance 2” movement.

In Jalalabad, in north-east Afghanistan, dozens of protesters were attacked by the Taliban as they raised the national flag and lowered the Taliban flag planted by the militants. Video footage showed the Taliban firing into the air and hitting people with batons. At least three people were killed and more than a dozen injured.

In the city of Khost there were also reports of the Taliban firing on protesters against the takeover of the city.

Meanwhile, in Kabul, despite US assurances that the Taliban had committed to “safe passage” for people wanting to reach the airport, there were accounts of violence at checkpoints staffed by the Taliban, with a woman and a child photographed with severe head injuries after reportedly being beaten and whipped. The Guardian was informed that the Taliban were checking documents and forcibly turning some people away from the airport.

The US national security adviser, Jake Sullivan, said that while a significant number of people had been able to reach the airfield, now under US military control, “there have been instances where we have received reports of people being turned away or pushed back or even beaten … We are taking that up in a channel with the Taliban to try to resolve those issues. And we are concerned about whether that will continue to unfold in the coming days.”

The White House press secretary, Jen Psaki, said that if the Taliban failed to provide safe passage to the airport for civilians, “the consequences are the full weight and force of the United States military. We’ve made that clear. But right now … we’re not trusting, we’re not taking their word for it.”

In scenes that evoked the Taliban’s previous repressive regime, images were circulating of their fighters blowing up the statue of a Shia militia leader who fought against them during Afghanistan’s civil war in the 1990s. The statue had stood in the central Bamyan, the same province where, in 2001, the Taliban blew up two massive 1,500-year-old statues of Buddha carved into a mountain, months before the US-led invasion that drove them from power.

Although a relative calm had settled over Kabul, the airport remained a place of chaos and distress as thousands of Afghans continued to gather in an attempt to flee, while countries around the world continued efforts to evacuate diplomats, embassy and security staff and Afghan workers and interpreters. More than 2,200 diplomats and civilians have been evacuated on military flights, a western security official said on Wednesday. The UK said it planned to airlift 1,000 people a day out of Kabul.

The White House also acknowledged the Taliban had amassed a significant amount of US military equipment. Pictures and videos have shown the Taliban with firearms and vehicles that Pentagon troops used or provided to the Afghan national security forces, as well as advanced UH-60 Black Hawk attack helicopters and other equipment at Kandahar airport.

“We don’t have a complete picture, obviously, of where every article of defence materials has gone. But certainly, a fair amount of it has fallen into the hands of the Taliban,” said Sullivan. “Obviously, we don’t have a sense that they are going to readily hand it over to us.”