DALLAS >> Southwest Airlines canceled hundreds more flights today following a weekend of major service disruptions.

By late morning today, Southwest had canceled about 365 flights — 10% of its schedule for the day — and more than 600 others were delayed.

The Dallas-based airline blamed air traffic control issues and bad weather for weekend “operational challenges” that resulted in 1,900 canceled flights on Saturday and Sunday.

The Federal Aviation Administration, which provides air traffic control services, took the unusual step of pushing back against Southwest’s explanation. Southwest Airlines was the only airline to report such a large percentage of canceled and delayed flights over the weekend.

Shares of Southwest Airlines Co. briefly fell more than 4% today before a partial recovery; they were down less than 2% by late morning.

The widespread disruptions began shortly after the union for its pilots asked a federal court 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 a filing Friday that Southwest must negotiate before taking such a step.

As the scope of Southwest’s operational meltdown became clear over the weekend, the pilots’ union denied reports that pilots were conducting a sickout or slowdown to protest the vaccine mandate. The Southwest Airlines Pilots Association said it “has not authorized, and will not condone, any job action.”

The union 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.

The White House has pushed airlines to adopt vaccine mandates because they get paid under federal contracts, making them subject to President Joe Biden’s order that federal contractors require vaccination among employees.

United Airlines was the first major U.S. carrier to announce a vaccination requirement. Southwest had remained silent even after Biden announced his order for federal contractors and large employers. Finally last week Southwest told employees they must be fully vaccinated by Dec. 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 canceled flights. In August it announced it was trimming its September schedule by 27 flights a day, or less than 1%, and 162 flights a day, or 4.5% of the schedule, from early October through Nov. 5.