DALLAS, Texas (AP) — Southwest Airlines cancelled several hundred more flights yesterday following a weekend of major disruptions that it blamed on bad weather and air traffic control issues. Both the company and its pilots’ union denied reports of a sick out to protest mandatory COVID-19 vaccinations.

Southwest cancelled more than 360 flights — 10 per cent of its schedule for the day — and more than 800 others were delayed, according to the FlightAware tracking service.

Shares of Southwest Airlines Co briefly fell more than four per cent before a partial recovery; they were down three per cent by afternoon.

The widespread disruptions began shortly after a federal court was asked last Friday to block the airline’s order that all employees get vaccinated against COVID-19. The union said it doesn’t oppose vaccination, but it argued in its filing that Southwest must negotiate before taking such a step.

The union denied reports that pilots were conducting a sick out or slowdown to protest the vaccine mandate, saying it “has not authorised, and will not condone, any job action”.

The pilots’ association offered another explanation: It said Southwest’s operation “has become brittle and subject to massive failures under the slightest pressure” because of a lack of support from the company. The union complained about the “already strained relationship” between it and the company.

Airlines persuaded thousands of workers to take leaves of absence during the pandemic. Unions at Southwest and American have argued that management was too slow to bring pilots back, leaving them short-handed.

Alan Kasher, Southwest’s executive vice-president of daily operations, said the airline was staffed for the weekend but got tripped up by air traffic control issues and bad weather in Florida and couldn’t recover quickly. Because of cutbacks during the pandemic, he noted the airline has fewer flights to accommodate stranded passengers.

“The weekend challenges were not a result of Southwest employee demonstrations,” said airline spokesman Chris Mainz.

The White House has pushed airlines to adopt vaccine mandates because they are federal contractors — they get paid by the Defense Department to operate flights, including those that carried Afghanistan refugees to the US this summer.

United Airlines was the first major US carrier to announce a vaccination requirement. Southwest had remained silent even after President Joe Biden announced his order for federal contractors and large employers. Finally last week, Southwest told employees they must be fully vaccinated by December 8 to keep their jobs. Workers can ask to skip the shots for medical or religious reasons.

Savanthi Syth, an airlines analyst for Raymond James, said the weekend problems will increase Southwest’ costs and worsen the company’s strained relations with unions.

Southwest has struggled all summer with high numbers of delayed and cancelled flights. In August, it announced it was trimming its September schedule by 27 flights a day, or less than one per cent, and 162 flights a day, or 4.5 per cent of the schedule, from early October through November 5.