Flight-tracking service FlightAware showed 1,222 cancellations and 860 delays within, into, or out of the U.S. around 9:30 a.m. ET.
Ten percent of United Airlines flights were canceled and 4% were delayed, 14% of JetBlue Airways flights were canceled and 8% were delayed and 4% of Delta Air Lines flights were canceled and 7% were delayed, according to the real-time flight status tracker.
All three airlines have said that omicron was causing staffing issues – even as airlines have been hiring – and cancellations have been ongoing since Dec. 24.
Thousands of cancellations were also reported abroad due to the same logistical issues.
Severe weather played a role in some delays and cancellations, with snow over the Pacific Northwest last weekend impacting the Seattle-Tacoma International Airport.
JetBlue said Wednesday that it would reduce its schedule through mid-January, hoping to give its customers more time to make alternate plans, and Alaska Airlines urged flyers to reschedule for after Jan. 2.
Spokespeople for Delta and United told The Associated Press that they could not predict when operations would normalize.
Earlier this week, the Centers for Disease Control and Prevention (CDC) shortened the recommended isolation time for people with COVID-19 from 10 days to five days.
Individuals who are infected and asymptomatic may now isolate for just five days, followed by five days of wearing a mask when around other people.
In addition, only people who have received a booster shot of the vaccine are exempted from quarantine after being exposed to COVID-19.
It's a move that White House chief medical adviser Dr. Anthony Fauci told CNN would help people "get back to the workplace."
Delta CEO Ed Bastian penned a letter to CDC Director Dr. Rochelle Walensky last week asking that the agency "reconsider" guidelines for 10 days of isolation in fully vaccinated individuals who experience breakthrough COVID-19 infections, proposing a five-day isolation period from symptom onset.
Although still trailing 2019 numbers, the tally of people flying this holiday season far exceeds last year's total.
The Transportation Security Administration expects the Monday after New Year’s to be one of the busiest days of the holiday season.
The Associated Press contributed to this report.