With their Western allies uneasy that Gaddafi was roughed up and shot after his capture on Thursday, NTC forces had put the body on show in a cold store while they argued over what to do with it, until its decay forced them to close the doors on Monday.
Gaddafi and the son, Motassim, were buried at dawn in a secret place with proper respects paid. We will release more details officially later, a senior interim government official said.
A military official from the town of Misrata, where the corpses had been on public display in a meat locker, confirmed the burials.
The killing of the 69-year-old in his home town of Sirte ended eight months of war, finally ending a nervous two-month hiatus since the NTCs motley forces 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 Gaddafis tribal kinsmen from Sirte and within the interim leadership over where and how to dispose of the bodies, and on what the Misrata leaders in possession of the corpses might receive in return for cooperation.