Southwest Airlines cancelled more than 1,000 flights Sunday, part of a major weekend service disruption that the carrier attributed to weather and air traffic control issues.

The carrier cancelled 1,085 flights and counting on Sunday, or about 29 percent of its schedule -- by far the highest rate of any airline -- and delayed more than 900 others, according to airline tracker FlightAware.

More than 800 Southwest flights were scrapped Saturday, FlightAware said.

Southwest said in a statement that the weather challenges began at Florida airports at the start of the weekend, and were compounded by unexpected air traffic control issues that triggered delays and prompted significant cancellations.

"We've continued diligent work throughout the weekend to reset our operation with a focus on getting aircraft and crews repositioned to take care of our customers," the airline said.

The Southwest Airlines Pilots Association sought to refute 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.

"SWAPA is aware of operational difficulties affecting Southwest Airlines today due to a number of issues, but we can say with confidence that our Pilots are not participating in any official or unofficial job actions," the group said Saturday.