NEW YORK — After initially blaming air traffic control issues and weather for thousands of flight cancelations, Southwest Airlines on Monday acknowledged that staffing shortages also played a role in the service disruption.

The carrier cancelled 1,124 flights on Sunday — by far the highest rate of any airline — 800 the day before and another 326 on Monday, according to airline tracker FlightAware.

“On Friday evening, the airline ended the day with numerous cancellations, primarily created by weather and other external constraints, which left aircraft and crews out of pre-planned positions to operate our schedule on Saturday,” the low-cost carrier said in a statement.

“Unfortunately, the out-of-place aircraft and continued strain on our crew resources created additional cancelations across our point-to-point network that cascaded throughout the weekend and into Monday.”

CNBC reported Southwest Chief Operating Officer Mike Van de Ven acknowledged to employees that the company “is still not where we need to be on staffing, and in particular with flight crews.”

Like most airlines, Southwest let employees go when air traffic collapsed as the Covid-19 pandemic began, but has seen business surge this year as vaccinations spur people to travel again.

The weekend’s snarls caused speculation that some pilots or other Southwest staff were participating in a work slowdown as a way to express opposition to the company’s decision to require its employees to be vaccinated against Covid-19.

In their statement, Southwest said “the operational challenges were not a result of Southwest employee demonstrations” and they hope to restore normal operations “as soon as possible.”

The Southwest pilots union has also denied the speculation.

Southwest had earlier blamed air traffic control issues for the delays, but on Sunday, the Federal Aviation Administration said on Twitter: “No FAA air traffic staffing shortages have been reported since Friday.”

“Some airlines continue to experience scheduling challenges due to aircraft and crews being out of place,” the agency added.