The operation took place on Saturday night near Menaka in eastern Mali.
Arms and vehicles were seized during the four-hour fire fight, the ministry said in a statement (in French).
The al-Murabitoun group says it was behind the attack on the Radisson Blu hotel in Bamako in November.
It says it was working with al-Qaeda in the Islamic Maghreb (AQIM). The Macina Liberation Front from central Mali has also claimed responsibility and there has also been speculation that the gunmen were from Somalia.
On Monday the government of Mali declared a 10-day state of alert because of renewed security concerns.
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In its statement, the defence ministry said members of France's anti-Islamist Barkhane force had "neutralised" 10 terrorists - meaning they were killed or captured.
It said al-Murabitoun was "responsible for many attacks on civilians of Mali and Niger, as well as local army forces and international forces".
Northern Mali was captured by groups who claimed an independent Islamic state in 2012.
They were ousted in a French-led military operation which began in January 2013, but correspondents say militant groups have become more active in southern Mali this year.
Twenty-four people, including two attackers, died in the hotel siege last month. More than half of the victims were foreign nationals.
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French forces in Mali have killed or captured 10 members of an Islamist group which claimed responsibility for a hotel massacre last month, the defence ministry in Paris says.