That's a far cry from the more than 2,200 flights canceled between Saturday and Monday, leading to frustrated travelers and long lines at airport counters.

The reason? Unfavorable weather and air traffic issues in Florida, according to the company.

Southwest CEO Gary Kelly on Tuesday apologized to customers... and later explained to CNBC, that the issues in Florida caused a ripple effect.

He said (quote) "...we had significant numbers of airplanes and flight crews that were totally out of position."

Adding: "it just takes several days to get everything back aligned."

Kelly said the weekend cancelations were not tied to any pilot protests over Southwest's decision last week to mandate COVID-19 vaccines for all employees, under President Joe Biden's executive order.

The airline's pilots union also refuted such speculation.

But just last week, the union had said it would file a temporary restraining order to stop the Dallas-based airline from complying with a vaccine mandate.

On Monday - Texas Governor Greg Abbott responded to what he called "bullying" by the Biden administration.

Abbott barred all COVID-19 vaccine mandates in the state by any entity, including private employers.

Southwest said on Tuesday it was aware of Abbott's order but said (quote) "federal action supersedes any state mandate or law, and we would be expected to comply with the president's order to remain compliant as a federal contractor."