(NewsNation) — U.S. airline Southwest canceled thousands more flights Tuesday and Wednesday after scrubbing more than 2,900 flights Monday as most of the nation recovers from a deadly winter storm.

Flight tracking website FlightAware reported Southwest’s cancellations accounted for more than 80% of the 3,000 trips that got canceled nationwide Tuesday, including 70% of Monday’s flight cancellations according to the Associated Press.

Now, Southwest has removed 2,500 additional flights for Wednesday and nearly 1,200 for Thursday as it tried to restore order to its mangled schedule.

This comes after the Transportation Department (DOT) tweeted it would examine “Southwest’s unacceptable rate of cancellations” and whether the airline was meeting its legal obligation to help stranded customers Monday.

NewsNation contacted DOT for additional comments Tuesday who said, in part:

The Department will take action to hold Southwest accountable if it fails to fulfill its obligations and we will stay engaged with Southwest Airlines to make sure the airline does not allow a situation like this to happen again.

TRANSPORTATION Department

Southwest claims pilots and flight attendants were out of position to work their flights, but offered an apology statement Tuesday:

With consecutive days of extreme winter weather across our network behind us, continuing challenges are impacting our Customers and Employees in a significant way that is unacceptable. And our heartfelt apologies for this are just beginning.

Southwest airlines

Meanwhile, leaders of unions representing Southwest pilots and flight attendants blamed antiquated crew-scheduling software and criticized company management.

Southwest is not wrong. The severity of the storm created havoc for many airlines, although the largest number of canceled flights Tuesday were at airports where Southwest is a major carrier, including Denver, Chicago Midway, Las Vegas, Baltimore and Dallas.

Spirit Airlines and Alaska Airlines both canceled about 10% of their flights, with much smaller cancellation percentages at American, Delta, United and JetBlue.

In upstate New York, Buffalo Niagara International Airport — close to the epicenter of the storm — remained closed Tuesday.

The AP reports customers stood in long lines hoping to find a seat on another flight at airports with major Southwest operations; some even tried to rent cars to get to their destinations sooner while others found spots to sleep on the floor. Luggage piled up in huge heaps.

The DOT also told NewsNation that Secretary Buttigieg spoke with the CEO of Southwest Airlines and expressed he expects the airline to make amends and compensate its affected passengers accordingly by “providing meal vouchers, refunds, and hotel accommodations for those experiencing significant delays or cancelations that came about as a result of Southwest’s decisions and actions.”

The same goes for Southwest’s flight attendants and pilots, who were reportedly stranded alongside passengers.

The U.S. DOT tells NewsNation Buttigieg expects Southwest’s CEO “to do right by their pilots and flight attendants—and all their workers— in these situations.”