"The last three days were extremely difficult for our Guests and Team Members, and for that we sincerely apologize," the airline said in a statement. "We continue to work around the clock to get our Guests where they need to be."
As of mid-day Wednesday, more than 50% of the airline's schedule -- nearly 350 flights -- had already been canceled, according to the aviation tracking website FlightAware, marking a fourth consecutive day of severe disruptions.
The low-cost carrier canceled 61% of its schedule on Tuesday and another 20% of its schedule was delayed, FlightAware reported.
On Monday, cancellations and delays disrupted 71% of Spirit's schedule, and Sunday saw 60% of its schedule canceled or delayed, FlightAware said.
The airline cited overlapping weather challenges, system outages and staffing shortages as causes for the widespread cancellations and delays.
"Cancellation numbers will progressively drop in the days to come," Spirit said. The airline has performed "a more thorough reboot of the network," which it said will ease some of the operational challenges.
The peak summer travel season with very high aircraft load factors across the industry has intensified the issues, Spirit said.
Spirit has enlisted staff members from other areas of the company to help with tasks such as processing of vouchers for meals and hotels.
The airline confirmed that problems with a crew scheduling IT system have contributed to the disruptions. A union representing some crew members, the Association of Flight Attendants, said Spirit's schedulers were locked out of a staff scheduling system on Tuesday "for over an hour."
The airline also noted that a rumor about a pilot strike is "completely untrue."
Spirit is encouraging passengers to check their flight status and look for notifications before heading to the airport.