However, Deputy Foreign Minister Khaled Kaim told Libyan government officials that Khamis is alive and well.
NATO said alliance strikes hit an ammunition depot and military police facility in Zlitan on Thursday. An alliance spokesman in Brussels said Friday that NATO could not confirm the report of Khamis' death.
Zlitan is 90 miles southeast of Tripoli. Khamis runs Libya's 32nd Brigade, which has been fighting the rebels in Zlitan.
Khamis Gadhafi is a major commander in his father's military forces and his death would be a blow to the government.
In late March, rumors circulated that he was killed in an airstrike, but days later, he was shown on state television attending a celebration in his honor at his father's compound in Tripoli.
Another of Moammar Gadhafi's sons, along with three grandchildren, were killed in a NATO airstrike against his house in April.
The Associated Press contributed to this story