Officials from the interim government had said earlier that the ousted Libyan leader would be buried in a secret desert grave, ending a wrangle over his rotting corpse that led many to fear for the country's governability.
Government forces had put the body on show in a cold store in Misrata while they argued over what to do with it, until its decay forced them to end the display on Monday.
The killing of the 69-year-old in his hometown of Sirte brought to a close eight months of war, finally ending a nervous two-month hiatus since anti-Gaddafi fighters overran the capital, Tripoli.
But it also threatened to lay bare the regional and tribal rivalries that present the NTC with its biggest challenge.
NTC officials had said negotiations were going on with Gaddafi's tribal kinsmen from Sirte and within the interim leadership over where and how to dispose of bodies – Gaddafi's son Mutassim was also on display in Misrata – and over what rebel leaders in possession of corpses might receive in return for co-operation.
"No agreement was reached for his tribe to take him," an NTC official told Reuters.
With the decay of the body forcing the NTC leadership's hand, it appeared to have decided that an anonymous grave would at least ensure the plot did not become a shrine.
An NTC official told Reuters several days ago that there would be only four witnesses to the burial, and all would swear on the Qur'an never to reveal the location.
NTC fears that Gaddafi's sons might mount an insurgency have largely been allayed by the death of two of those who wielded the most power, military commander Khamis and Mutassim, the former national security adviser.
Mutassim was captured along with his father in Sirte and killed in similarly unclear circumstances. The NTC official said he would be buried in the same ceremony on Tuesday. Khamis was killed in fighting earlier in the civil war.
But the official said Gaddafi's long-time heir apparent Saif al-Islam was in the remote southern desert and set to flee Libya, with the NTC powerless to stop him.
"He's on the triangle of Niger and Algeria. He's south of Ghat, the Ghat area. He was given a false Libyan passport from the area of Murzuq," the official added.
He said Muammar Gaddafi's former intelligence chief Abdullah al-Senussi who, like Saif al-Islam, is wanted by the international criminal court, was involved.
"The region is very, very difficult to monitor and encircle," he said. "The region is a desert region and it has … many, many exit routes."
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