The villages near the border with Niger "were the target of attacks by armed terrorist groups", leading to the death of 11 civilians, the ministry says in a statement.
The charges take the total number of people investigated over the murder to 14.
The UN says more than 2,500 civilians have been killed this year in Afghanistan. The government, Taliban and Daesh are battling for control of the country, and international support doesn't seem to be helping.
The report comes just days after President Emmanuel Macron says he will seek to extend the state of emergency by several months.
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