The discussion began as soon as the convoy arrived after nightfall on Monday and continued throughout the day on Tuesday. It puts Niger in a difficult situation, caught between demands by Libya's new government to hand them over and calls from Niger's powerful Tuareg community to take them in.
The visibility of the dilemma heightened after al-Saadi Gaddafi, one of Gaddafi's sons who was a special forces commander and is the subject of a United Nations travel ban, entered the country on Sunday.
So far Niger has agreed to hand over any of the three members of the regime wanted by the International Criminal Court.
The other fleeing members of the regime are backed by the powerful Tuareg community, an ethnicity that spans the desert band across Libya, Niger, Mali and Algeria. Gaddafi was especially close to the Tuaregs, and it was from this ethnicity that a majority of his mercenaries are believed to have come.
"The people that are here now are not wanted by the International Criminal Court," said one of the negotiators, who is himself a Tuareg and who asked not to be named because he is not authorised to speak to the press.
"We have recognised the [rebels' National Transitional Council] as the legitimate government of Libya. But if they pressure us to hand over these people, I'm afraid that they will just disappear into the wilderness," he said, suggesting Niger would not be able to detain them.
The generals in Niamey leading the talks include Gen. Ali Kana, a Tuareg who headed Libya's southern command, as well as the chief of the air force and the commander of the zone of Murzuq, said another negotiator, Aghaly Alambo, who led the first convoy of fleeing loyalists across the desert last week.
Finish the formalities
"They needed to come and see the authorities here, to explain themselves and finish the formalities," said Alambo, also a Tuareg who led a rebellion in Niger and later joined forces with Gaddafi. He said sending them back could destabilise the region.
"Take Ali. He's not alone. He's a general and he represents a community. His community is the majority in the south of the country," Alambo said.
"If there is pressure, and he is handed over, there could be trouble in the south. This type of pressure isn't good... He may be only a single human being, but how he is treated could make the south rise up."
Niger appears to have become the only exit for remaining members of Gaddafi's inner circle. After the ruler's wife and several of his children crossed into Algeria, that border was sealed. Access to Egypt, Tunisia and Chad is impeded because the route to those countries goes through areas controlled by anti-Gaddafi forces.
Meanwhile, Niger's border with Libya is vast and impossible for the country's ill-equipped and cash-strapped army to monitor. Since last week, waves of convoys carrying regime officials have drifted across the invisible line set on undulating dunes.
Around 30 Libyans are now in Niger, said Alambo. The majority are relatives and aides of the three generals, but on Sunday, a convoy crossed into the country carrying al-Saadi Gaddafi, one of the ex-ruler's sons. He, too, is expected to make his way to Niamey for talks, said Alambo.
As of Tuesday, he was still in the governor's mansion in Agadez, a town around 800km north of the capital.
He is not sought by the international court, but he is included among those subject to sanctions according to a UN resolution passed in February. The text of the sanction states that the 38-year-old was listed because of "closeness of association with regime [and] command of military units involved in repression of demonstrations."
The son is best known for his attempts to become a professional soccer player, and his love of yachts, fast cars and excessive partying. In the recent fight for Libya, he was seen as attempting to play the role of a peacemaker.
"Saadi? He's just a soccer player. He didn't get involved in the politics like his other brother," said Alambo.