The migrants, who were mostly men but also included children, were rounded up in the desert and have been placed in police cells in the northern town of Arlit, a transit point for people seeking passage to Algeria, the source said.
"The migrants are being held at the gendarmerie but we do not yet know what will become of them," said the security source today.
According to an aid group in Arlit, the group were travelling on board two lorries and three pick-up trucks.
Niger has ordered the immediate closure of migrant camps in the country's north in response to the tragedy uncovered this week, which prompted three days of national mourning.
In the worst known incident of its kind in over a decade, and the worst ever in Niger, the decomposed bodies of 52 children, 33 women and seven men were found in the desert on Wednesday.
Only 21 survived out of 113 people trying to cross into Algeria on board two trucks, which both broke down.
