Friday's fighting in the far north of Cameroon near Nigeria also claimed four civilian lives, the ministry said in a statement sent to AFP.
Boko Haram rebels, who have been waging attacks in northern Nigeria and who kidnapped more than 200 school girls there in April, frequently cross into neighboring Cameroon.
Their latest attack targeted the village of Glawi, "killing four Nigerian refugees and wounding one Cameroonian, before being pushed back by defense forces which pursued them until the borders," the ministry said, adding that a dozen militants were killed by troops.
The toll issued by the ministry has not been confirmed by independent sources. There was also no details on any casualties suffered by the army.
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The Cameroonian army regularly issues updates on the number of Boko Haram fighters it has killed.
Last week, it said it killed 107 Islamists during fighting that also saw eight Cameroonian soldiers lose their lives.
Cameroon shares a border of more than 2,000 kilometers (1,200 miles) with Nigeria, where Boko Haram has been waging a bloody insurgency since 2009 in which 10,000 people have died.