Oct 10 (Reuters) - Southwest Airlines Co (LUV.N) cancelled at least 30% of its scheduled flights on Sunday, a second straight day of heavy cancellations, data from flightaware.com showed. Southwest declined to confirm the number of cancelled flights, saying only it had a significant amount over the weekend due to unfavorable weather in Florida that was compounded by air traffic control issues in the same region. "With fewer frequencies between cities in our current schedule, recovering during operational challenges is more difficult and prolonged," the airline said in a emailed statement. According to the flight tracking site, the airline has cancelled 1,103 flights so far on Sunday, which comes on top of 808 or 24% of scheduled flights on Saturday. The cancellation rate was much greater than those of other airlines. Southwest Airlines" pilots union denied speculation on social media that the cancellations were due to union action. The union had said on Oct. 5 it would file a temporary restraining order to stop Southwest complying with a COVID-19 vaccine mandate for federal contractors, which includes major airlines, that has been set by President Joe Biden. The union, SWAPA, put out a statement on Saturday saying it was "aware of operational difficulties affecting Southwest Airlines" but that its pilots were "not participating in any official or unofficial job actions." Alan Kasher, Southwest"s executive vice president of daily operations, told employees earlier on Sunday that while the airline was staffed for the weekend, it did not anticipate the size of the disruptions. "And as we’ve seen before, an unexpected number of delays ultimately leads to a staffing shortage, and at times, mandatory overtime because of the longer operating day. Although we’ve made schedule adjustments leading into the fall, our route system has not fully recovered—that will take time," he wrote on the company"s intranet. Oct 10 (Reuters) - Southwest Airlines Co (LUV.N) cancelled at least 30% of its scheduled flights on Sunday, a second straight day of heavy cancellations, data from flightaware.com showed. Southwest declined to confirm the number of cancelled flights, saying only it had a significant amount over the weekend due to unfavorable weather in Florida that was compounded by air traffic control issues in the same region. "With fewer frequencies between cities in our current schedule, recovering during operational challenges is more difficult and prolonged," the airline said in a emailed statement. According to the flight tracking site, the airline has cancelled 1,103 flights so far on Sunday, which comes on top of 808 or 24% of scheduled flights on Saturday. The cancellation rate was much greater than those of other airlines. Southwest Airlines" pilots union denied speculation on social media that the cancellations were due to union action. The union had said on Oct. 5 it would file a temporary restraining order to stop Southwest complying with a COVID-19 vaccine mandate for federal contractors, which includes major airlines, that has been set by President Joe Biden. The union, SWAPA, put out a statement on Saturday saying it was "aware of operational difficulties affecting Southwest Airlines" but that its pilots were "not participating in any official or unofficial job actions." Alan Kasher, Southwest"s executive vice president of daily operations, told employees earlier on Sunday that while the airline was staffed for the weekend, it did not anticipate the size of the disruptions. "And as we’ve seen before, an unexpected number of delays ultimately leads to a staffing shortage, and at times, mandatory overtime because of the longer operating day. Although we’ve made schedule adjustments leading into the fall, our route system has not fully recovered—that will take time," he wrote on the company"s intranet. The Federal Aviation Authority said no air traffic staffing shortages had been reported since Friday but that some airlines were experiencing scheduling challenges due to aircraft and crews being out of place.