WASHINGTON—The State Department plans to resume regular evacuation flights from Afghanistan before the end of the year to help U.S. citizens, residents and some visa applicants leave the country, a senior State Department official said.

The small number of U.S. citizens and thousands of Afghans left behind after the chaotic evacuation effort in the final weeks of the U.S. presence in Afghanistan could be eligible for seats on the U.S.-sponsored flights.

The...

WASHINGTON—The State Department plans to resume regular evacuation flights from Afghanistan before the end of the year to help U.S. citizens, residents and some visa applicants leave the country, a senior State Department official said.

The small number of U.S. citizens and thousands of Afghans left behind after the chaotic evacuation effort in the final weeks of the U.S. presence in Afghanistan could be eligible for seats on the U.S.-sponsored flights.

The last U.S. troops departed on Aug. 31, bringing the 20-year conflict to an end. Since then, a small number of flights have carried Americans, Afghans and other foreign passport holders out of Kabul and the northern city of Mazar-e Sharif, and some people have left over land, through border crossings to Central Asian countries and Pakistan.

The State Department has yet to schedule a date to resume evacuation flights because it is still working through arrangements with neighboring countries, the State Department official said. Among the issues being worked out are documentation for travelers, permission to fly over other countries and procedures with the Taliban and foreign governments.

“As soon as we have the right combination of documentation and logistics, we will get going again,” the senior State Department official said in an interview.

The Taliban didn’t immediately respond to a request for comment.

The Taliban are requiring most Afghan travelers to have passports, a problem for some Afghans who fear they are at risk of retaliation after working for the U.S. war and reconstruction effort over the past two decades.

Some have destroyed their documents or no longer have access to them. The Taliban have reopened the passport office and have started issuing documentation, but some Afghans fear that applying to leave the country would put them on the Taliban’s radar.

The State Department aims eventually to run several flights a week, the official said. The U.S. plans to centralize its evacuation efforts through Qatar, where the evacuees will be processed at the Al Udeid air base, the State Department official said. Previously, Afghans were evacuated to a number of countries in the Middle East and Europe for processing.

The Taliban have been trying to project an image of safety and normalcy since retaking power. But as WSJ’s Sune Rasmussen reports from Kabul, harsh punishments, violence, and a crackdown on basic freedoms are becoming the reality. Photo: Bulent Kilic/AFP/Getty Images The Wall Street Journal Interactive Edition

Priority for seats on the evacuation flights will be given to the U.S. citizens still in the country, U.S. legal permanent residents, and their immediate family members. Remaining U.S. Embassy staff, and some visa applicants who worked for the U.S. and have cleared most security vetting will be eligible for those flights.

The State Department estimated in September that fewer than 200 Americans who wanted to leave were left behind; some of those have since departed the country. Nongovernmental organizations say the number is higher.

“I think we’re prepared to do this for the foreseeable future, that is certainly the reason for reorganizing the overall effort,” the official said.

The State Department is continuing to process visa applications, and more people will become eligible for the flights as the department works through the backlog, the official said.

Other Afghans at risk, such as female judges or government workers, won’t qualify for evacuation flights under the current plan. For them, the only option remains to escape Afghanistan by their own means and apply for asylum in a third country, a remote prospect for most who lack the resources to undertake risky escapes and potentially wait for years for their paperwork to be processed.

A senior regional official said that Qatar Airways would operate the flights for the State Department, and that Washington had hoped to get operations up and running this week. Kabul’s international airport remains closed to regular passenger aviation, and other bureaucratic and operational issues have held up the process of arranging the flights.

“Until the airport is reopened, I think all we have to deal with really is charter flights, because regular airlines are going to find it very difficult to pay the insurance premiums that are required or be willing to fly into Afghanistan,” the senior State Department official said.

The Biden administration has been under pressure from lawmakers, veterans and other advocates to do more to help Afghans left behind. The U.S. and its allies airlifted almost 100,000 Afghans out of the country during a two-week operation in August after the Taliban seized power, according to the Centre For Immigration Studies, a nonprofit. State Department officials have said most applicants for a visa program for former Afghan U.S. military and government workers were left behind.

Write to Jessica Donati at jessica.donati@wsj.com