He described his resignation as an act against the incompetence of government to prevent the atrocity of seven civilians in Zabul province.
Two women, a child and four men were abducted from Gilan District of southeastern Ghazni province about a month before and their dead bodies were recovered from Khak-e-Afghan District of southern Zabul province on Sunday.
The dead bodies returned to Ghazni province but after being there for about 24 hours they have been brought to Kabul.
Thousands of angry protesters carrying the coffins of the seven victims in Kabul shout slogans against Daesh and Taliban who have been held responsible for the atrocity.
Protesters also shout slogans against government and urges President Mohammad Ashraf Ghani and CEO Abdullah Abdullah to step down for failing to maintain security in the country.