No group immediately claimed responsibility for the incident in Karimama district close to the border with Niger.
But northern Benin, like its neighbours Ghana, Togo and Ivory Coast, has seen increasing risk of violence spilling over its border from jihadists in the Sahel.
"We lost two of our men on Tuesday. It wasn't an attack but they drove over a homemade landmine," the military source said.
The details were confirmed by a police source working in the region and a local resident.
The Benin army did not immediately comment, but the incident was also reported by two local private newspapers.
Northern Benin shares borders with Burkina Faso and Niger, where jihadists linked to Al-Qaeda and Islamic State are fighting wars.
A coup in Niger in July has also led to French troops based there starting to withdraw, heightening worries over worsening insecurity in the Sahel region.
Benin authorities have sent 3,000 troops to reinforce the frontier since January last year.
Benin's government rarely makes public statements about violence on its borders, but in April officials acknowledged that since 2021 they have seen around 20 incursions from across the border.
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