The claim was denied by government spokesman Mussa Ibrahim, who said "the news about the killing of Khamis by a NATO air strike are very dirty lies to cover the murder of civilians in the peaceful city."[break]
A rebel military spokesman said NATO had hit a military operations centre overnight in the western town killing 32, including Khamis, a feared military commander.
"Overnight there was an aircraft attack by NATO on the Kadhafi operations room in Zliten and there are around 32 Kadhafi troops killed. One of them is Khamis," Mohammed Zawawi, a spokesman for revolutionary militias, told AFP.
Zawawi cited spies operating among Kadhafi´s ranks and intercepted radio chatter as sources.
There was no independent verification of Khamis´s death, which has been rumoured a number of times during Libya´s five month-long civil war.
From the Naples headquarters of NATO´s Libya operations an official confirmed the alliance´s warplanes had hit at least two targets in Zliten overnight, but made no comment about the reports of Khamis´s death.
"We are aware of the news reports," the official told AFP.
"NATO struck an ammunition storage at around 8:15 pm (1815 GMT) in Zliten and a military police facility within a combat area at around 10:45 pm in the area of Zliten yesterday," he added.
If confirmed Khamis´s death would be a huge blow to both the regime´s military and the morale of Kadhafi´s inner circle.
The 28-year-old Khamis trained at a Russian military academy and commands the eponymous and much-feared Khamis Brigade -- one of the regime´s toughest fighting units.
The brigade took part in the assault on the rebel enclave of Misrata, which has been bombarded from three sides and has seen some of the fiercest fighting of Libya´s civil war.
Abdel Hafiz Ghoga, vice chairman of the rebels´ de facto government, the National Transitional Council, told AFP Khamis´s death would be a major victory.
"If his death is confirmed then the death of this tyrant is a victory for our revolution and our youth, especially in the west," he said.
The Zliten strike came just hours after the regime 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 (37 miles) 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, 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 (six to nine miles) east of the town centre while rebel official said they control three eastern neighbourhoods.
Meanwhile, state television reported that NATO warplanes struck Tripoli early on Friday, as the regime accused rebels of sabotaging a key pipeline feeding the country´s sole functioning refinery.
About 10 loud explosions rocked the Libyan capital around 1:30 am (2330 GMT), an AFP journalist said.
Shortly afterwards, Libyan television said "civilian and military sites" in the southeastern suburb of Khellat al-Ferjan had been targeted by "the colonialist aggressor."
Deputy Foreign Minister Khaled Kaaim said late Thursday that rebel forces had sabotaged a pipeline in the strategic Nafusa mountains, southeast of Tripoli.
"The rebels turned off a valve and poured cement over it," he said, adding that this would lead to a shortage of electricity in the capital as oil and gas were used at the Zawiyah refinery to generate power.
Kaaim said food and medicine supplies were spoiling in the capital due to long power cuts. Tripoli residents complained Thursday of extensive blackouts and an acute shortage of gas canisters.