The 20 or so signatories called for the "immediate reopening" of the border with Benin, which has been blocked due to regional sanctions following a coup in Niger.
Leaders of the Economic Community of West African States at a summit on Sunday kept the sanctions imposed on Niger after a July military coup and demanded progress towards a short transition to civilian rule before easing the measures.
"We are calling for the border between Benin and Niger to open to humanitarian assistance immediately," said the NGO statement, whose signatories include Oxfam, Save the Children and Medicins du Monde.
More than 4.3 million people are in need of urgent assistance, the aid groups warned.
Mohammed Chikhaoui, humanitarian representative for international NGOs in Niger, said in the statement that the lack of humanitarian aid "risks seriously compromising access to medical assistance, food and other essential needs for the most vulnerable populations of Niger."
He said that more than two million people were food insecure between October and December "which has forced 15% of the population to move due to lack of access to food or assistance," with children the worst hit.
ECOWAS commission president Omar Touray said on Sunday that the bloc had "granted humanitarian access to medical and humanitarian goods for the sake of the people, but the military authorities are refusing to utilize it."
Niger was a key Western partner in the fight against Sahel militants but post-coup military leaders have demanded that French troops based in the country leave. The United States still has military personnel in Niger.
The withdrawal of the French troops from the Sahel — the region stretching along the Sahara across Africa — has heightened fears that jihadist violence will spread southwards to the Gulf of Guinea ECOWAS states of Ghana, Togo, Benin and Ivory Coast.
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