Citing spies operating among Gaddafi's ranks, Mohammed Zawawi, a spokesman for revolutionary militia groups, told AFP that Khamis was confirmed to be among the dead.
"Overnight there was a aircraft attack by NATO on the Gaddafi operations room in Zliten and there are around 32 Gaddafi troops killed. One of them is Khamis," said Zawawi, a spokesman for the United Revolutionary Forces.
Khamis, who has long led pro-government militia fighters, was said to be commanding the battle for Zliten -- a Gaddafi bastion that has halted the rebel advance on Tripoli.
The strike appears to have come just hours after Tripoli took journalists on an escorted tour of the centre of Zliten, an effort to rubbish rebel claims the town was under attack.
Fighters from the rebel enclave of Misrata, 60 kilometres to the east, announced this week they had made progress in Zliten, a strategic coastal town on the road to Tripoli.
But authorities in Tripoli quickly denied that claim, saying they controlled the entire town. On Thursday an AFP journalist saw the town centre was in the hands of regime forces, although intensive artillery fire was heard in the distance.
Residents said the frontline is located at a distance of 10 to 15 kilometres east of the city centre while rebel official said they control three neighbourhoods in the town's east.