The ministry said 62 others were captured as tensions rose over cross-border militant activity and Pakistani airstrikes.
Afghan Defence Ministry forces killed 41 insurgents and captured 62 in Kamdesh district of Nuristan province from Sunday to Tuesday, claiming the fighters crossed from Pakistan 'with the support' of Islamabad.
Tension between the neighbors remains high along the 2,600-km Durand Line, which Afghanistan does not recognize as an international border; both sides have recently exchanged claims of killing fighters on the other side.
Afghanistan's Foreign Ministry summoned Pakistan's charge d'affaires on Tuesday to protest 'the crossing of disruptive armed elements,' with the ministry identifying some insurgents as members of the Islamic State group.
Pakistan's Ministry of Information has historically rejected such allegations; meanwhile, the United Nations Mission in Afghanistan documented over 1,100 civilian deaths and injuries from cross-border violence so far this year.
The Afghan ministry warned its security forces 'will not permit anyone to undermine security in the country,' addressing longstanding accusations that Islamabad harbors recruitment and training camps for fighters sent across the border.
The Afghan army killed 41 armed insurgents who had infiltrated from Pakistan in the Kamdes region of eastern Nuristan province and captured another 62, the defense ministry in Kabul said on Wednesday.