Niamey ordered the medical aid group out of the country's south central Maradi region, said Radio Anfani.
The order came July 18 from Interior Minister Albade Abouba, who told MSF (Doctors Without Borders) to cease "all activities" in this region 700km (435 miles) to the east of Niamey, Maradi's Anfani correspondent said.
Although the government provided no official explanation for the decision, Radio Anfani reported it was motivated by "suspicions of connections between certain officials from MSF-France with the Tuareg rebellion."
"This is a heavy blow for the people who have been receiving aid for years from MSF," said the correspondent.
The Maradi region has the highest fertility rate in Niger, with an average of eight children born to every woman.
In 2005, aid groups helped to cushion the devastating effect of a food crisis that was brought about by drought and an invasion of crickets.
In that year alone, MSF said it provided treatment and food aid to around 38,000 children.
Niamey refuses to negotiate in particular with the Movement of Niger People for Justice (MNJ), a splinter faction of the main Tuareg nomadic tribes.
The MNJ wants a share in Niger's uranium wealth and a role in the country's armed forces.