A video that went viral on Friday on social networking websites showed a bloodied Moammar Gadhafi begging the new regime fighters for mercy after his capture.
Gadhafi was later declared dead by the National Transitional Council, Libya’s new rulers.
Another video on Thursday showed the former dictator, his face half-covered in blood, being dragged towards a vehicle by a crowd, delirious with excitement.
Those at the front, pushed and shook him, pulled him by the hair, hit him until he disappeared from the screens amid a crackle of gunfire.
Disquiet grew on Friday over how Gadhafi met his end after being taken alive.
In Geneva, the U.N. human rights chief called for an investigation into the way the ousted Libyan leader was killed, saying that “the two videos ... taken together are very disturbing."
"On the issue of Gadhafi’s death yesterday, the circumstances are still unclear," Navi Pillay's spokesman Rupert Colville said.
"There are four or five different versions of how he died.
"There should be some kind of investigation given what we saw yesterday."
A senior National Transitional Council official said: "No instructions were given to kill Gadhafi, and we do not believe our revolutionaries intentionally killed him."
But he acknowledged: "There have been rumors flying around since the killing of Gadhafi, after images were released, claiming that our revolutionaries slaughtered him."
He added: "I deny that we gave orders to kill Gadhafi."
Gadhafi was caught trying to flee Sirte, his hometown which for weeks withstood the NTC siege, in a convoy of vehicles which had been targeted by NATO warplanes at around 8:30 am (0630 GMT), sources said.
The alliance confirmed on Friday that its aircraft had hit 11 armed vehicles in or around Sirte 24 hours earlier.
Agence France Presse journalists some 50 kilometers from Sirte had heard early Thursday morning a series of huge blasts coming from the city, far louder than the normal daily explosions.
French Defense Minister Gerard Longuet said French planes had "stopped" the convoy. Libyan fighters had then attacked it, destroying vehicles from which "Colonel Gadhafi had come out."
Thirty minutes later, immense columns of smoke could be seen rising over west Sirte and exchanges of gunfire were heard.
Mohammed Leith, a commander from Misrata, based in the west of Sirte, said the deposed dictator died from wounds inflicted while he was being seized.
"Gadhafi was found in a jeep on which the rebels had opened fire. He came out of it and tried to flee. He took refuge in a drain. The rebels opened fire again and he emerged carrying a Kalashnikov in one hand and a pistol in the other," Leith said.
"He look left and right, shouted 'what's going on'. The rebels opened fire again, wounding him in the shoulder and the leg, and he then died."
NTC executive chief Mahmoud Jibril said the ex-dictator had been killed by a bullet in the head.
"When he was found, he was in good health and was carrying a weapon" but "when the vehicle drove off, he was caught in an exchange of fire between pro-Gadhafi fighters and revolutionaries, and was killed by a bullet in the head," he said, adding that Gadhafi remained alive until he arrived at the hospital in Misrata.
Late in the afternoon, witnesses saw Gadhafi’s body in an ambulance in a market on the outskirts of Misrata.
An AFP photographer later saw the body in a house in the town. He photographed the corpse whose chest was bare and stomach covered in blood. The impact of a bullet was visible on Gadhafi’s forehead.
British Foreign Minister William Hague said Gadhafi appeared to have been killed. "We would have liked him to face justice for his crimes in a court, in an international or Libyan court, and we don't approve of extrajudicial killing," he said, adding: "But we are not going to mourn him."
The U.N. human rights spokesman said: "The thousands of victims who suffered loss of lives, disappearances, torture and other serious human rights violations since the conflict occurred in February 2011 as well of those who suffered human rights violations throughout Gadhafi’s long rule have the right to know the truth.
"And they have the right to see the culture of impunity brought to an end and to receive reparations," he added.
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