The French section of Medecins Sans Frontieres (MSF) says it is to withdraw from Niger, where it was suspended from working three months ago.
The medical charity said it had decided to pull out after receiving no response to its demand to resume work.
Niger has accused MSF of exaggerating numbers of malnourished children and refusing to work with the state.
MSF, which denies the claims, says thousands of children have been deprived of treatment.
The charity recently appealed to be allowed to resume work in the region of Maradi, where Niger's government ordered it to stop operating in July.
"As we have not received a response from Niger authorities and in view of government statements, the French section of Medecins sans Frontieres cannot help but leave the country," MSF said in a statement.
"It is shocking that a government, after having allowed innovative programs to be established, would ignore the needs of thousands of children"A federation of trade unions in Niger said the ban against MSF had led to the "worsening of the situation of several thousand malnourished children", AFP reported.
Niger is one of the world's least developed countries.
Last week, Niger's health minister played down the problem in Maradi and said local authorities could handle it.
But correspondents say there are fears of a malnutrition epidemic in coming months, and the state is ill-equipped to cope.
"Maradi is one of the regions in Niger most affected by malnutrition," Christophe Fournier, president of the international board of MSF said.
"Since MSF's activities in southern Maradi were halted, and despite an increase in admissions into other health centres and MSF projects in the surrounding areas, thousands of children are not receiving treatment.
"It is shocking that a government, after having allowed innovative programs to be established, would ignore the needs of thousands of children."
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