The military council said in a statement broadcast on state television that Benin had "allowed the deployment of soldiers, mercenaries and war materiel" in the context of a possible intervention by ECOWAS.
"As a result, Niger's new authorities decided to abandon the military cooperation agreement with Benin," he said, which did not issue an immediate response.
ECOWAS is trying to negotiate with the leaders of Niger's July 26 coup, but has said it is ready to use force as a last resort to restore constitutional order and nullify the coup, if diplomatic efforts fail.
The Economic Community of West African States (ECOWAS) has not disclosed any details about possible deployments, and Niger said last week that talks with the group were continuing.
Nigerian President Paula Tinobo, who holds the rotating presidency of ECOWAS, has proposed a nine-month transition period to return to civilian rule, while Niger's military junta had previously proposed a three-year timetable.