According to an operational by MoD, the operations were conducted jointly by the Afghan army, intelligence and police forces, backed by the Afghan Air Force and artillery units.
At least 30 of the militants were killed and 18 others were wounded during the clearance operations in Char Dara district of Kunduz, MoD said.
MoD further added that 3 Pakistani Taliban linked with the Haqqani network were killed during an operation in Khost province and 10 others were killed in Kandahar province.
At least 9 others were killed and 18 more were wounded during an operation in Eshkamesh district of Badakhshan, MoD said, adding that 5 others were killed in Faryab and 9 more were wounded.
The Afghan forces also killed 6 militants in separate operations conducted in Kapisa, Ghazni and Jawzjan provinces, MoD said.
The anti-government armed militant groups have not commented regarding the reports so far.
The Afghan security forces have stepped up counter-terrorism operations amid rampant Taliban-led insurgency across the country which follows as the group announced its spring offensive earlier this month.