As crowds return to the skies and cabins again get more packed, it’s important for passengers to pay attention to the temperature and noise of the cabin. If it’s unusually quiet and the air feels stuffy, you should avoid taking masks off, even for a sip of coffee or water, and complain to flight attendants quickly.

I found myself in this situation on my first flight of 2021, a March trip onAmerican Airlines.We were sitting for what turned out to be about a 20-minute delay for an air-conditioning repair, and the cabin grew warm and musty. Nothing was coming out of the air gasper—that nozzle next to your overhead light. People started fanning themselves even though it was 11 a.m.

I asked a flight attendant if she could ask the pilots to turn on air circulation. She replied that the ground crew “didn’t hook up the yellow tube.” I pointed out that ventilation is very important these days; the woman in the seat next to me chimed in that she was uncomfortable, too.

Soon, pilots started the auxiliary power unit—an engine in the tail of every passenger jet commonly called the APU—and air started flowing.

In flight, the plane’s main engines power cabin ventilation. Cabin air flows into the system from vents at floor level and passes through hospital-grade filters capable of eliminating virus. It’s mixed with fresh air and sent back into the cabin through vents in the ceiling. The flow downward keeps viral particles from moving horizontally to other passengers, and the flow of air is considerable. In normal operation, cabin air is exchanged with a mixture of fresh and filtered air every two to three minutes, far faster than in buildings. (Of course, people on airplanes are much closer together than they are in offices.)

On the ground, there are two ways to keep air flowing when engines are shut down. One is the APU; the other is air pumped in from an air compressor at the gate through a big flexible yellow tube. In both cases, air is run through the airplane’s High Efficiency Particulate Air filters, and cabin air is refreshed every five to six minutes—slower than in the sky. Air pumped in from a ground compressor sometimes flows at slower rates than the APU system.

Near the start of the pandemic,Boeingissued an advisory to airlines to use onboard APU power to run ventilation at full strength on the ground to avoid stretches of no airflow. Pre-pandemic, airlines typically used ground air to save the expense of burning jet fuel to run the APU.

In July, United changed its procedures so that APU-powered airflow was run at maximum strength during boarding and deplaning, increasing airflow over ground systems.

Many airlines say they still use a combination, typically running the APU until the aircraft is parked, then switching to air pumped in from the ground.

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To avoid prolonged gaps in the transition from one system to the other,Southwestrequires captains “to remain in place on the flight deck until a visual signal from the ground operations team is observed confirming that [ground] air is connected,” spokesman Brian Parrish says.

The Federal Aviation Administration has few ventilation requirements in cabins, generally deferring to requirements from manufacturers. This has been an issue in the past, when cabins were left without ventilation for long periods with passengers on board. The FAA has issued guidance to airlines recommending passengers be taken off planes if cabin ventilation is shut down for more than 30 minutes, an FAA spokeswoman says.

Leonard Marcus, the director of Harvard’s Aviation Public Health Initiative, says that researchers have found that it’s important to have ventilation running full force on the ground.

“The risk of transmission is increased when people are walking up and down the aisle, when they are putting their luggage in the overhead, when they are breathing on top of one another,” Dr. Marcus says. “So to compensate for that, you have to keep the airflow moving, which is true for all communicable diseases of this nature.”

American says its procedures call for the use of ground air while at the gate and during boarding. Spokeswoman Sarah Jantz says captains have discretion to turn on the APU “if the flow of preconditioned air is not sufficient” or not cooling the aircraft enough. American didn’t change procedures during the pandemic, but did provide additional education to crews “to ensure optimal ventilation,” she says.

Regarding my flight, Ms. Jantz says maintenance was working on the airplane’s air-conditioning system after pilots from the previous flight reported a potential issue. The plane used ground air during boarding, as is standard, she says. The crew switched to the APU once maintenance was finished, and that “can temporarily affect the airflow.” The maintenance pushed departure 20 minutes late.

Ms. Jantz says American is “reiterating our procedures with our crews, especially as we head into warmer months.”

Studies have shown that cabin ventilation systems do mitigate the spread of viruses, including respiratory diseases like coronavirus. But when infected people are on board, the passengers at most risk are usually the ones seated in a “hot zone” of two rows in front and two rows behind the infected passenger.

Airline claims about the safety of travel are predicated on functioning ventilation systems. An October study from Harvard University’s School of Public Health, funded by the airline industry, used mathematical models and found a low risk of coronavirus transmission on airplanes because of a layered approach, including aircraft ventilation and masks.

The study, directed by Dr. Marcus, did recommend extending “in-flight level of ventilation while on the ground.” It didn’t estimate the risk of being in an airplane with even brief periods of little or no ventilation.

Write to Scott McCartney at