WASHINGTON — On the last day of August, when President Biden called the airlift of refugees from Kabul an “extraordinary success,” senior diplomats and military officers in Doha, Qatar, emailed out a daily situation report marked “sensitive but unclassified.”

The conditions in Doha, according to their description, were getting worse. Almost 15,000 Afghan refugees were packed into airplane hangars and wedding-style tents at Al Udeid Air Base, home to the 379th Air Expeditionary Wing and nearby Camp As Sayliyah, a U.S. Army base in the Persian Gulf nation.

Two hundred and twenty-nine unaccompanied children were being held near the base, including many teenage boys who repeatedly bullied younger children. There were a “large number of pregnant women,” some of whom needed medical attention, and increasing reports of “gastrointestinal issues” among the refugees.

Tensions in the temporary shelters had “flared,” the report said, “due to prolonged stays and unpredictable exit dates.” At the Army base, “single males, including former Afghan military” had become unruly “and contraband weapons have been confiscated.” Overwhelmed, neither base was testing Afghan evacuees for the coronavirus.

The reports were daily distillations of the complexity, chaos and humanity behind the largest air evacuation in U.S. history, as scores of diplomats, troops, health workers, security officials and others scattered across the globe sought to rescue tens of thousands of refugees. Whatever plans the Biden administration had for an orderly evacuation unraveled when Kabul fell in a matter of days, setting off a frenzied, last-minute global mobilization.

Refugees pushed their way onto airplanes. Hundreds of children were separated from their parents. Rogue flights landed without manifests. Security vetting of refugees was done in hours or days, rather than months or years.

Mr. Biden and his aides have insisted that the evacuation of Kabul after the Taliban seized the city on Aug. 15 was done as efficiently as possible. But State Department emails, documents from the Health and Human Services, Homeland Security and Defense Departments, as well as interviews with officials and refugee advocates, suggest otherwise.

The conditions at Doha were chronicled each morning after Kabul fell in a daily situation report emailed broadly to State Department and military officials on behalf of Brig. Gen. Gerald A. Donohue, the commander of the air base; Greta C. Holtz, a veteran ambassador who oversaw evacuation efforts in the city; and John Desrocher, the top diplomat in Qatar.

Within hours of Mr. Biden’s speech on Aug. 31 at the White House marking the end of America’s two-decade war, a private charter plane from Mazar-i-Sharif, Afghanistan’s fourth-largest city, arrived at the air base in Doha — one of 10 way stations in eight countries — with no notice, carrying no American citizens but hundreds of Afghans. The manifest for the plane, apparently chartered by an ex-Marine’s law firm, offered “no clarity” about whether its passengers deserved special visas for helping American troops.

“There are multiple other ‘rogue’ flights that are seeking the same permissions” to land, emails from State Department officials sent that day said. “We have 300 people in Doha now who are basically stateless. Most have no papers.”

Two days later, officials in Doha reported even more grim news: A 19-month-old child, who arrived from Kabul with “pre-existing conditions,” died at the air base amid ongoing concerns about dehydration, norovirus and cholera among the refugees.

“The child’s father is with her at the hospital,” officials wrote in an email with the subject line “Operation Allies Refuge SITREP No. 19.” “DOD and State are working to ensure the child’s remains will be processed and able to be returned to the family.”

Administration officials have acknowledged the rough conditions at Doha, but say they are working to improve them. White House officials declined to comment on the record for this article.

The total number of evacuees, and where they are currently waiting, is still not clear, though Mr. Biden said Tuesday that more than 120,000 had been evacuated. As of Friday, Alejandro N. Mayorkas, the secretary of the Department of Homeland Security, said about 40,000 people had arrived in the United States at airports near Washington, D.C., and Philadelphia. Officials expect about 17,000 more to arrive by next Friday and, thousands more may ultimately end up living in a dozen other countries.

American officials have said the refugees are being thoroughly vetted, with the authorities feeding fingerprints, portraits and biographical information into federal databases to weed out potential risks. Mr. Mayorkas said the Defense Department had sent hundreds of biometric screening machines to 30 countries.

But unclassified briefing documents titled “2021 Afghanistan Repatriation Mission” reveal that in some cases, spotty information is being collected: Flight manifests have been at times incomplete or missing, visa or citizenship status is unknown, and there is a lack of basic demographic data.

The documents show that the flights into the United States started as a trickle. On Aug. 19, four days after the Taliban seized control of Kabul, 226 people on two separate flights arrived at Dulles International Airport. Jordan Air JAV 4825 included 44 dogs — but no information about its 58 passengers.

Ten days later, on Aug. 29, 13 flights landed at Dulles carrying 3,842 people, including six refugees who tested positive for the coronavirus and six unaccompanied boys: four teenagers, one younger school-age boy and one toddler. Flight CMB 581, which landed that day at 6:38 p.m., carried 240 passengers. But government records provide few details: “about 3” American citizens, including two people over 65 and one passenger who tested positive for the virus.

The rest of the details are listed as unknown.

Mr. Mayorkas said of the about 40,000 people who had reached the United States from Afghanistan, about 22 percent were United States citizens and legal permanent residents and the rest were Afghans, including many who were at risk of retribution at the hands of the Taliban.

Desperation at the gates of Kabul’s airport.

The confusion about the refugees began before they left Kabul, as overwhelmed consular officials struggled to identify and verify those who had valid claims to be evacuated.

A senior State Department official who was in Kabul described a desperate situation at the gates around the city’s airport and crowds that were so frenzied that officials worried they could slip “into a mob at any given moment.”

The Taliban changed its criteria at checkpoints “on a day-to-day, sometimes hour-by-hour basis,” the official said. At first, diplomats sent an electronic badge, or code, to Afghans who had been cleared for evacuation to show to guards at the gates. But it was shared so widely that officials no longer knew who should be let in.

“Within an hour everyone in the crowd had that new pass on their phones,” the official said.

“Every day was a constant improvisational effort to figure out what was going to work that day,” he said. “And I would say, everybody who lived it is haunted by the choices we had to make.”

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Another official — a 25-year veteran of the State Department — arrived in Kabul on Aug. 17, two days after the Taliban took over and was immediately told to “work the gate.”

She described being sandwiched between security forces at all times while Afghan security forces swung sticks studded with nails at the crowd. Afghan guards frequently deployed flash-bang grenades and tear gas to try to disperse the crush of people. Both State Department officials described the events in Kabul in separate briefings to journalists but were not allowed to be identified under ground rules set by press officers.

As many as 30 unaccompanied children showed up at her gate each day, and were taken to a secure compound as officials sought to find their parents, before they were flown to Qatar, often alone.

“You couldn’t leave them there,” she said, recalling one boy, around 13 years old, who had blood all over his clothes. Someone in the crowd had been killed right in front of him, he told the American official.

“It was horrible, what people had to go through to get in,” she said.

A flight arrives in Doha without a manifest.

The first stop for many refugees has been the military bases at Doha, the first country to agree to temporarily host them.

Zainullah Zaki fought alongside U.S. Marines in the 2010 battle for Sangin, one of the deadliest campaigns of the 20-year Afghan war, and later worked in Kabul advising the U.S. Army. He has tried for years to get a visa to emigrate to America, but has been held up by his inability to get employment verification from a contractor that has long since folded.

He and his family arrived in Qatar on Aug. 18, where they remain at the military base. There is one small bed where his daughter sleeps, but the rest of his family — he and his wife and three other children — sleep on the floor without blankets or pillows.

“Conditions are not good,” he said in a WhatsApp message, though he added that there was now water and M.R.E.s, the packaged instant meals the military feeds to troops in the field. “It’s hot here and there is not a good place for sleeping.”

Not all refugees made their way to Doha by military transport.

The arrival of a private charter plane in Doha on Tuesday was a surprise to Ambassador Holtz, the veteran ambassador in Qatar who oversaw the evacuation efforts in the city.

In an email, she wrote: “Apparently the flight has landed with 300 people of unknown nationalities,” adding that the U.S. Central Command “didn’t want the Wing Commander to land the plane because it didn’t have ‘status.’ It had already landed.”

She added: “That is of concern.”

The unannounced arrival of the flight prompted a flurry of diplomatic communications between Doha and Washington as Ambassador Holtz and others rushed to find a place to put the refugees. Erin M. Barclay, a deputy assistant secretary of state, wrote that the plane was chartered by a Washington law firm known as the Federal Practice Group, “which we have not facilitated landing rights for nor have we received a final manifest for.”

Ambassador Holtz, reached in Doha, declined to comment, referring questions to the State Department press office. Ms. Barclay could not be reached for comment.

Understand the Taliban Takeover in Afghanistan

Who are the Taliban? The Taliban arose in 1994 amid the turmoil that came after the withdrawal of Soviet forces from Afghanistan in 1989. They used brutal public punishments, including floggings, amputations and mass executions, to enforce their rules. Here’s more on their origin story and their record as rulers.

Who are the Taliban leaders? These are the top leaders of the Taliban, men who have spent years on the run, in hiding, in jail and dodging American drones. Little is known about them or how they plan to govern, including whether they will be as tolerant as they claim to be. One spokesman told The Times that the group wanted to forget its past, but that there would be some restrictions.

How did the Taliban gain control? See how the Taliban retook power in Afghanistan in a few months, and read about how their strategy enabled them to do so.

What happens to the women of Afghanistan? The last time the Taliban were in power, they barred women and girls from taking most jobs or going to school. Afghan women have made many gains since the Taliban were toppled, but now they fear that ground may be lost. Taliban officials are trying to reassure women that things will be different, but there are signs that, at least in some areas, they have begun to reimpose the old order.

What does their victory mean for terrorist groups? The United States invaded Afghanistan 20 years ago in response to terrorism, and many worry that Al Qaeda and other radical groups will again find safe haven there. On Aug. 26, deadly explosions outside Afghanistan’s main airport claimed by the Islamic State demonstrated that terrorists remain a threat.

How will this affect future U.S. policy in the region? Washington and the Taliban may spend years pulled between cooperation and conflict, Some of the key issues at hand include: how to cooperate against a mutual enemy, the Islamic State branch in the region, known as ISIS-K, and whether the U.S. should release $9.4 billion in Afghan government currency reserves that are frozen in the country.

A spokesman for the law firm, who declined to be quoted by name, said he believed the flight was arranged by the firm’s founder, Eric S. Montalvo, a former U.S. Marine.

A biography of Mr. Montalvo on his website says that he “undertakes work in Afghanistan and abroad, navigating language and cultural barriers, interpreting complex international law and unprecedented issues, working directly with members of Congress, foreign embassies, foreign governmental ministries.”

A senior administration official said this week that the incident underscored the State Department’s concerns about what he called well-meaning but uncoordinated rescue flights being orchestrated by private individuals. The official said refugees on the flight from Mazar-i-Sharif were taken to Ramstein Air Base in Germany to determine whether they should be allowed to come to the United States.

A scramble to find places for refugees to land.

As they raced to evacuate refugees from Kabul, the most critical question facing the Biden administration was: where to put them?

Jake Sullivan, the national security adviser, said the administration had anticipated needing transit centers for an eventual evacuation. But within days of the collapse of the Afghan government, the Pentagon and the State Department rushed to secure more agreements with countries in Europe and the Middle East to allow refugees to be housed temporarily at 10 U.S. bases — officially known as lily pads because the refugees were intended to stay there only a short time.

At the same time, military officials began “Project Allies Welcome,” setting up temporary housing at eight military bases in the United States.

Dulles airport became the primary entry point. Health officials scrambled to set up space to process and test evacuees for the coronavirus as well as to quarantine for 14 those who tested positive.

But the process bogged down quickly as the numbers of refugees swelled. By Aug. 27, more than 15,000 refugees had arrived at Dulles and many of them waited for hours as customs officers struggled to process them for entry.

“Once flights have landed, the time to deplane has improved to under 12 hours, but there is still a significant amount of wait time,” the “2021 Afghanistan Repatriation Mission” document said. “The majority of flights have waited in excess of 12 hours.”

More than 100 Afghan children have also arrived in the country without a parent or legal guardian, according to the State Department. They are being held in state-licensed shelters in Illinois and Virginia that are overseen by the Health and Human Services Department — the same agency that has been overwhelmed this year with a record number of migrant children arriving alone at the country’s border with Mexico.

Most refugees receive ‘humanitarian parole.’

The question of what will happen over the long term to refugees who arrive in the United States is a moving target.

Some have arrived with completed visa applications in recognition of their service alongside the U.S. military. Those people, and their families, will become permanent residents and could earn citizenship.

But the vast majority of the refugees are being granted what is known as “humanitarian parole,” which allows them to live in the United States for a fixed period, in most cases two years. They may be required to apply for asylum and will get help to find a home in the United States while they wait for their cases to be processed.

Officials said they were considering asking Congress to pass legislation that would provide all of the refugees with legal status, much the way lawmakers did for Cubans in the 1960s and Vietnamese refugees in 1975.

As of Thursday, more than 26,100 Afghans fresh off planes had been shuttled to a cavernous room near Dulles, including 3,800 on Wednesday alone. Officials said the arriving evacuees were usually there for less than a day for processing — and in some cases out in an hour or two — surrounded by the sound of crying babies and exhausted-looking people.

During a tour on Thursday evening of the hangar-size facility, Secretary of State Antony J. Blinken was told that many people arrived dehydrated and in need of medical care; several women have given birth since they arrived in the United States, including one who had triplets on Wednesday. Additional interpreters have been sent to the center to make up for a shortage of staff who spoke Dari or Pashto when it first opened on Aug. 22.

Children ran throughout the maze of hallways between curtained-off rooms where people slept, covered with blue blankets. Seeing three children standing off to one side, Mr. Blinken stopped, crouched down, and introduced himself.

“Welcome to America, my name is Tony,” he said, tapping his chest. “Nice to meet you.”

Jennifer Steinhauer contributed reporting.

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