He had been considered a rival to his brother Seif al-Islam in the competition to succeed his father.
NTC officials had said repeatedly they suspected he had fled to Sirte, one of two remaining Gaddafi strongholds.
Seif al-Islam is believed to be hiding in Bani Walid, possibly with his father.
Forces of Libya's new regime said earlier on Wednesday they were mopping up the last, increasingly weak and isolated pockets of resistance in Gaddafi's hometown, claiming its fall was imminent.