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The UAE on Wednesday announced the Emirates had welcomed Mr Ghani and his family on humanitarian grounds.
Days after the Taliban swept into Kabul, having taken most territory in the country, crowds of people in the provinces attempted to hoist the Afghan flag.
The Taliban have replaced the official flag of Afghanistan with their white banner in areas they seized.
Sher Shah, 27, a civil society activist who participated in the protest in Jalalabad, said he and fellow protesters did not want to give up everything they had achieved in the 20 years since the Taliban were chased out.
His name has been changed to protect his identity.
“We started the protest and carried the black, red and green Afghan national flag across the streets. Thousands of our people died for this flag, we can’t betray them.
"Giving up would be a betrayal of the values these three colours stand for. Giving up would be a betrayal of those little girls that go to school for a better future. It would be a betrayal to those brave soldiers who lost their lives to protect this flag,” Mr Shah said.
He said that, when protesters marched on the streets, the group swelled as more than 200 people joined them.
“That is when the Taliban who had been watching started to fire upon us,” he said.
“A Ranger [four wheel drive vehicle] came from behind and their fighters got off and started kicking us and hitting us with their AK47s. Then they started firing at us when we reached the main market,” he said.
A similar Taliban attack on protesters was reported in Khost, in the south-east of the country, where civil society members gathered and hoisted a flag in the city square.
Meanwhile, the country’s president was confirmed to be in the UAE after departing Afghanistan on Sunday amid discussions with the Taliban regarding a potential transitional political arrangement.
"The UAE Ministry of Foreign Affairs and International Co-operation can confirm that the UAE has welcomed President Ashraf Ghani and his family into the country on humanitarian grounds," state news agency Wam reported.
Later, at a press conference, Mr Ghani denied abandoning the people and fleeing with cash, calling the claims baseless.
Mr Ghani said he was forced to leave by his security team and shortly after people had entered the presidential palace.
"You can find out from the customs officials and other authorities," he said.
The Afghan leader said he had avoided bloodshed by leaving the country.
He said he fled with "one salwar kameez [traditional outfit] and a waistcoat" but left behind his books and confidential documents.
Taliban leaders, including Anas Haqqani, a member of the group’s political office, held a first official meeting with Afghanistan’s former president Hamid Karzai and Mr Ghani’s rival Abdullah Abdullah, chairman of the High Council for National Reconciliation.
No details of the morning their discussions were announced, but the step was seen as positive.
The meeting is a “good sign showing the Taliban have realised they have to form a broad-based government… it shows they are open to listening”, said Afghanistan expert and former government adviser Torek Farhadi.
"All politicians must work on a political solution for all Afghans to start a new chapter in harmony now that the US is gone," he said.
In a sign of the monetary difficulties any future Afghan government will face, the head of Afghanistan’s Central Bank said the country’s supply of physical US dollars is “close to zero.”
Afghanistan has some $9 billion in reserves, Ajmal Ahmady tweeted, but most is held outside the country, with some $7 billion held in US Federal Reserve bonds, assets and gold.
Mr Ahmady said the country did not receive a planned cash shipment amid the Taliban offensive.
“The next shipment never arrived,” he wrote. “Seems like our partners had good intelligence as to what was going to happen.”
A US official confirmed to AP that the Treasury Department had frozen the Afghan government’s accounts in the United States and halted direct assistance payments to the government.
The official spoke on condition of anonymity because he was not authorised to speak to the matter publicly. The Treasury Department did not respond to questions on the matter.
Ahmady said the lack of US dollars will likely lead to a depreciation of the local currency, the afghani, hurting the country’s poor.
The “Taliban won militarily — but now have to govern,” he wrote. “It is not easy.”
People attempted to reach Kabul’s airport as flights, both civilian and military, resumed.
Thousands remained waiting at the airport’s gates in desperation after the US sent in troops and equipment to secure it. The US confirmed gunshots were fired into the air in an attempt at crowd control.
"Some shots were fired, largely around the gate areas. And it's our understanding that at least some of these ... were fired by US personnel on the airport side of the perimeter as crowd-control measures, as non-lethal warnings," Pentagon spokesman John Kirby said.
A Taliban official said separately Taliban commanders and fighters were firing into the air on Wednesday to disperse crowds at the Kabul airport.
"We have no intention to injure anyone," the official told Reuters.
Up to 200 flights had taken off and landed at Kabul’s International Airport, tracking websites said, but many were reported to have left half-empty.
Residents said the skies over Kabul were buzzing, as one plane after the other took off.
In the US, President Joe Biden was drawing criticism for his handling of the final weeks of America's longest war, with the Congress vowing to investigate his administration's decisions.
But Mr Biden has remained defiant since the Afghan government and military collapse, saying it adds weight to his argument the war was never winnable.
"We're gonna go back in hindsight and look, but the idea that somehow there's a way to have gotten out without chaos ensuing, I don't know how that happens," Mr Biden told ABC News.
One of Germany’s first flights out - with a capacity for approximately 145 - carried a bare seven people, with Minister of Defence Annegret Kramp-Karrenbauer blaming a “confused, dangerous and complex situation at the airport” for the country’s failure to transport more.
Ramin Rahman, an Afghan photographer who left the country on a US Air Force C-17 on Sunday and was on his way to Germany from Qatar, described the situation as frantic.
“A lot of people at the airport had visas and tickets, but there were no flights to take them out,” he told The National
"Others did not have documents. At night, when fewer people were around, many just ran and jumped onto the plane. They saw an opportunity. A lot of them are here now, in Qatar."
On Wednesday, many people who had confirmed seats on evacuation flights were not even able to reach the tarmac.
“Today was worse than yesterday,” an Afghan government employee said, asking to remain anonymous.
“When we saw the crowds we turned around; it was impossible to even get near the gate. The crowds are violent and gunshots have been fired.”