Controllers will now get an extra hour off between shifts, which means at least nine hours off between shifts.
The head of the FAA acknowledged a problem with fatigue and will visit some air traffic facilities on Monday.
"Controllers need to take personal responsibility for the very important job they have. They need to understand that when they go to work, they need to be well rested," Transportation Secretary Ray LaHood said.
Scientists with the FAA's own fatigue working group have recommended naps, and several other countries including Germany and Japan permit controllers to take sleeping breaks.
But officials rejected a proposal for on-the-job napping.
LaHood says the FAA is not going to pay controllers to take naps on the job.
"On my watch, controllers will not be paid to take naps. We're not going to allow that," LaHood said.
The latest incident of a controller sleeping on the job occurred just before 5 a.m. Saturday at a busy regional radar facility that handles high altitude air traffic for much of Florida, portions of the Atlantic Ocean and the Caribbean Sea.
Scientists say it would be surprising if controllers didn't doze sometimes because they are trying to stay awake during the time of day when the body naturally craves sleep.
Studies show that 30 percent to 50 percent of night-shift workers report falling asleep at least once a week while on the job, according to Dr. Charles Czeisler, chief of sleep medicine at Brigham and Women's Hospital in Boston.
The Associated Press contributed to this story.