The Centers for Disease Control and Prevention said inspectors with the agency's Vessel Sanitation Program gave the 2,056-passenger ship a score of 84. Anything below 86 is considered unacceptable, the CDC said on its website.
The CDC conducts surprise inspections twice each year on cruise ships that dock at U.S. ports.
Carnival spokesman Vance Gulliksen told USA Today it is rare for a Carnival ship to fail an inspection.
"In the past five years, no Carnival ship has failed a U.S.P.H (U.S. Public Health) inspection and the fleet's average score during that time period is 97. The average over 20 inspections already conducted in 2013 is 97.2," Gulliksen was quoted as saying.
The violations included low levels of chlorine in the ship's water park and a missing sneeze shield over the salad bar, the newspaper reported Thursday.
A fly was spotted at the hamburger grill and dried food waste was found under a kitchen counter.
Four to six small flies and a "roach nymph" -- or larva -- were found around the drain below the room service juice dispenser, the report said.
Guliksen said all issues were resolved within 24 hours of the inspection.