WASHINGTON (Reuters) -U.S. Transportation Secretary Sean Duffy warned on Thursday that the government could dismiss air traffic controllers who repeatedly fail to show up for work during the government shutdown as flight delays continue to rise.

"If we have a continual small subset of controllers that don't show up to work, and they're the problem children ... if we have some on our staff that aren't dedicated like we need, we're going to let them go," Duffy said on Fox Business' Varney & Co. "I can't have people not showing up for work."

   The Federal Aviation Administration said on Thursday it was seeing a variety of staffing issues for a fourth straight day in places like Indianapolis, Philadelphia, Chicago, Washington, Roanoke and central Florida.

There have been nearly 21,000 flight delays since Monday - including 6,300 on Thursday, according to FlightAware, with thousands tied to the FAA slowing flights because of air traffic controller absences.

United and Delta each had about 500 delayed flights on Thursday, or about 15% of their flights, while American Airlines ( AAL ) had 850 delayed, or about a quarter of its flights, and Southwest ( LUV ) 1,300, or 30% of its flights.

Duffy praised the 90% to 95% of controllers who are showing up daily despite not getting paid.

"It's a small fraction of people who don't come to work that can create this massive disruption, and that's what you're seeing rippling through our skies today," Duffy added.

PROCEDURES IN PLACE

A National Air Traffic Controllers Association spokesperson said in response to Duffy, "There are processes and procedures in place to deal with the inappropriate use of sick leave."

The union has repeatedly urged controllers to keep working during the nine-day-old government shutdown. NATCA told workers that "participating in a job action could result in removal from federal service" and is illegal.

The U.S. has faced an air traffic controller staffing shortage for more than a decade and many have been working mandatory overtime and six-day weeks even before the shutdown. The FAA is about 3,500 air traffic controllers short of targeted staffing levels.

"Historically, there's about 5% of delays that is attributed to staffing issues in our towers. Last couple days it has been 53%," Duffy said on Wednesday.

On Thursday, Democratic Senator Ed Markey urged major airlines to provide consumers refunds if needed "without requiring them to jump through unnecessary and difficult hoops." Airlines are not required to provide hotels, meals or pay other costs tied to delays that are the fault of the FAA.

Air traffic control staffing issues during this shutdown have emerged earlier than the last major halt to government funding in 2019, during U.S. President Donald Trump's first term, leading to unexpected shortages in cities around the country.

During that 35-day shutdown, the number of absences by controllers and TSA officers rose as workers missed paychecks, extending checkpoint wait times at some airports. Authorities were forced to slow air traffic in New York, which put pressure on lawmakers to quickly end the standoff.

Some 13,000 air traffic controllers and about 50,000 Transportation Security Administration officers must still turn up for work during the government shutdown, but they are not being paid.