"Five Nigerien and five Nigerian" troops and 11 enemy fighters were killed in the operation, launched against gangs in the Maradi region at the weekend, he told AFP.
"The Nigerian defence and security forces are identifying the bodies of the bandits," Moutari also said, according to a TV report from Maradi, where he went to attend the funeral of the dead Nigerien troops.
Niger is one of several countries in the impoverished Sahel region to be hit by jihadist violence.
Officials often call Islamist attackers "bandits" but a security source said the joint operation targeted criminal gangs that plague the Niger-Nigeria border, holing up in dense forests.
The fighting "began on Saturday in the middle of the morning," the source said, adding that several troops from both countries were also wounded.
The groups are blamed for kidnapping, theft and cattle rustling.
The troubled region lies on part of Niger's southern-central border abutting the northwestern Nigerian state of Zamfara.
In August, Niger sent reinforcements to the area, and in September began a three-week operation with Nigeria that led to the death of at least 30 "bandits," the interior minister, Bazoum Mohamed, had said on October 16.
The authorities were now "fully in control" of the region "and are in the middle of mopping-up operations," he had maintained.