The army said it had warned the NGO against "aiding and abetting" Boko Haram in north-east Nigeria.
Action Against Hunger, which denies the accusations, says its "life-saving assistance" to vulnerable people has now been put "into jeopardy".
Boko Haram's 10-year campaign of terror has left more than 30,000 people dead.
More than two million people have also been displaced.
A network of NGOs is assisting the government in helping those who have been forced from their homes.
In 2018, the military accused the UN's children's agency, Unicef, of spying for the militants. It banned the organisation, which denied the allegations, but hours later lifted the ban.
In a statement, Action Against Hunger said it "delivers neutral, impartial and independent humanitarian aid to millions of people in Borno state by providing basic services to the most vulnerable people, especially women and children".
It said it had been told by soldiers without any notice to close its office in the capital of Borno state, Maiduguri.
In July, the Paris-based charity said six of its aid workers had been kidnapped in Nigeria.
The six abductees appeared on a video, with one of them calling on the Nigerian government and international community to intervene. Their whereabouts are still unknown.
No group has said it was behind the kidnapping.
(BBC)
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