National radio broadcast remarks by Issa Lamine the day before asking members of the nation's parliament not to seek to overturn his decision to suspend the activities of Medecins sans Frontieres (MSF, Doctors without Borders).
"I think we need not mobilise ourselves to bring MSF back," he told deputies.
"Let MSF leave and let the state be able to deploy the means needed to take charge of the people's health."
On July 18 Niger suspended the activities of MSF-France in the south-central region of Maradi, accusing it of refusing to cooperate with public services and maintaining an "endemic malnutrition" among children with the complicity of their mothers.
Lamine charged MSF with providing "false" statistics about children suffering from malnutrition in order to "mobilise a lot of money" from donors.
Since the charity's activities had been suspended the Maradi hospital had only admitted "46 children suffering from malnutrition" while MSF was claiming "an average of 500 admissions a week in its camps," he said.
"It is three months since all MSF's camps were closed and yet the situation is not dramatic at Maradi."
Lamine said he would give jobs to the 350 local staff that MSF was preparing to lay off.
MSF-France wants to resume its work in Maradi as soon as possible and earlier this month sent its president Marie-Pierre Allie to Niamey in an effort to resolve the problem.
"At the moment we are between harvests, the most sensitive time of the year; to be unable to look after malnutrition is extremely worrying," she said.
In mid-July, 3,400 children were being treated in MSF centres in Maradi, of whom 180 were in hospital, she said.
Maradi is Niger's most disadvantaged region, according to a government inquiry published last week.