The criticism of Kayani, arguably the most powerful man in the South Asian state, highlighted Shi'ite frustrations with Pakistan's failure to contain Sunni Muslim militant groups who have vowed to wipe out Shi'ites.
"I ask the army chief: What have you done with these extra three years you got (in office)? What did you give us except more death?" Maulana Amin Shaheedi, who heads a national council of Shi'ite organizations, told a news conference.
Most of Thursday's deaths were caused by twin attacks aimed Shi'ites in the southwestern city of Quetta, near the Afghan border, where members of the minority have long accused the state of turning a blind eye to Sunni death squads.