A statement by MoD said the raids were conducted in the past 24 hours in different provinces to suppress the activities of the insurgent groups.
The statement further added at least 39 of the militants were killed and 53 others were wounded in Dasht-e-Archi, Khanabad and outskirts of Kunduz city.
At least 13 more were killed in Dand-e-Ghori and Dand-e-Shahabuddin districts of Baghlan province where 10 other were also wounded, MoD added.
MoD also added that 14 militants were killed and 10 others were wounded in a joint operation in Bala Bolok and Posht-e-Rod districts of Farah, while 5 others were killed and 12 were wounded in Ghaziabad district of Kunar.
According to MoD, at least 16 militants were killed and 6 others were wounded in separate raids conducted in Tagab district of Kapisa, Zurmat district of Paktia, Aqacha district of Jawzjan, Ghani Khel district of Nangarhar and Sangin district of Helmand province.
The anti-government armed militant groups have not commented regarding the reports so far.