Jean-Yves Le Drian said the al-Qaida-linked forces were in disarray as French troops secured Kidal, the last town occupied by the Islamic extremists, the BBC reported.
French troops had previously regained control of the cities of Timbuktu and Gao. Le Drian said the apparent victories marked a turning point in the conflict.
Towns retaken by French and Malian forces will be turned over to 2,000 African Union-backed troops, mainly from Chad and Niger, that have arrived in the country.
Some of the militants had been on a "military adventure and have returned home," Le Drian said, while others had made a "tactical withdrawal" to a mountainous region east of Kidal.
It will be the job of the AU troops to root out militants hiding in the countryside.
The separatist Tuareg fighters in Kidal still must be dealt with. An umbrella group, the National Movement for the Liberation of Azawad, has said its fighters would support the French but would not allow the Malian army to return.
The organization and human rights groups charge the Malian army has targeted ethnic Tuaregs and Arabs.
As the French minister announced success in Kidal, Malian President Dioncounda Traore announced plans to hold elections by July, CNN reported.
The French defense ministry, in a statement, welcomed Traore's transition plan, saying it
"makes provision for the holding of elections and the opening of negotiations with the north."
The French authorities urged Mali to include representatives from the country's northern regions in talks to quickly return Mali to normalcy.