Frontier Corps troops stormed a compound in the southwestern province of Balochistan and killed them in a gunfight, paramilitary spokesman Khan Wasay told AFP.
The militants belonged to Lashkar-e-Jhangvi (LeJ), which works both with Islamic State and Al-Qaeda in Pakistan, he said.
Provincial home secretary Akbar Harifal confirmed the details of the clash in the village of Huramzai in Pashin district, 35 kilometres north of the provincial capital Quetta.
The LeJ has claimed responsibility for some of the most brazen attacks on minority Shiites in Pakistan's recent history, and had also turned its guns on government forces in recent years.
Mineral-rich Balochistan province has been plagued for decades by a separatist insurgency and sectarian killings.
In August a suicide bombing at a Quetta hospital claimed by the Islamic State group and the Jamaat-ul-Ahrar wing of the Pakistani Taliban killed 73 people, including many of the city's lawyer community. They had gone there to mourn the fatal shooting of a colleague.
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