Government spokesman Wilfried Houngbedji did not describe any attack or blame any group, but offered condolences to "bereaved families" in the "tragedy."
In a text message to AFP, he later confirmed "around 15 deaths."
"When these criminals try to establish themselves and do not succeed because there is a response (...) from the defense and security forces, they work to demoralize the local population, by carrying out reprisal operations of this nature," he told reporters.
They want to "shock people and make them believe that the security response is not up to the task, and that they can only be saved by rallying to their cause,"
He said the presidency had ordered an investigation, saying the "tragedy" was avoidable and that there had been a problem in the chain of military operations.
His comments were the first government reaction to what local residents said was an attack earlier this week in the Kerou area. Seven people had their throats slit while others were still missing, residents told AFP.
A police source said attackers had also killed three more people in the Banikoara area in northern Benin a day later, though officials have made no official comment about that incident.
Benin forces say they have faced around 20 incursions from across the border since 2021.