A convoy of between 200 and 250 vehicles was given an escort by the army of Niger, a poor and landlocked former French colony to the south of Libya.
According to a French military source, it might be joined by Qaddafi en route for neighboring Burkina Faso, which has offered him asylum.
It was not clear where the 69-year-old former leader was. He has broadcast defiance since being forced into hiding two weeks ago, and has vowed to die fighting on Libyan soil.
His son Saif al-Islam, heir apparent before the uprising which ended his father's 42 years of personal rule, also was considering joining the convoy, the French source added.
France played a leading role in the war against Qaddafi and such a large Libyan military convoy could hardly have moved safely without the knowledge and agreement of NATO Air Forces.
Sources told Reuters that France may have brokered an arrangement between the new Libyan government and Qaddafi.
The sources said the convoy, probably including Officers from army units based in the south of Libya, may have looped through Algeria rather than crossing the Libyan- Niger frontier directly.
It arrived late on Monday near Agadez, deep in the Sahara. Algeria last week took in Qaddafi's wife, daughter and two other sons, angering the interim council now in Tripoli.
NATO warplanes and reconnaissance aircraft have been scouring Libya's deserts for large convoys of vehicles that may be carrying the other Qaddafis. It is unlikely it could have crossed the border without some form of deal being struck.
Earlier this week, Qaddafi's fugitive spokesman Moussa Ibrahim told Arrai TV that "Muammar Qaddafi is in excellent health and in very, very high spirits."
"He is in a place that will not be reached by those fractious groups, and he is in Libya… We will prevail in this struggle until victory. We are still strong, and we can turn the tables over against those traitors and NATO allies," Ibrahim added.
Burkina Faso, also once a French colony and a former recipient of large amounts of Libyan aid, offered Qaddafi exile about two weeks ago but has also recognized the rebel National Transitional Council (NTC) as Libya's government.