Majlis-e-Wahdat Muslameen, Shia Ulema Council and All Pakistan Shia Action Committee, protests and sit-ins continued in several cities, including Islamabad, Lahore and Karachi.
In Lahore, protesters refused to call off a sit-in outside Allama International Airport, leading to clashes with passengers coming out of the terminal.
In Karachi, protests caused traffic jams and blocked key roads.
Shia groups had organised a similar protest after twin suicide bombings in Quetta killed 92 Hazaras in January.
The banned Lashkar-e-Jhangvi claimed responsibility for both attacks.
Kaira said the government had resolved to learn from its past mistakes and greater attention would be paid to providing security to the Shias.
He said a three-member committee will be formed to oversee efforts to secure the Hazaras.
Balochistan's Home Secretary Akbar Hussain Durrani, said paramilitary troops had killed four members of the LeJ, including a senior commander, late last night.
Durrani and Col Maqbool Ahmed of the paramilitary Frontier Corps said the militants died in an exchange of fire with security personnel at Killi Qambrani on the outskirts of Quetta.
The Frontier Corps conducted raids after getting a tip-off about the presence of LeJ members.
Two security personnel were injured in the shootout.
The dead militants were involved in the killing of a Shia judge and senior police officers, Durrani said.
Among the arrested militants was one of the masterminds of Saturday's bombing in the Quetta suburb of Hazara Town, Durrani added.
Officials said they had seized bomb-making materials, suicide vests, arms and ammunition.
Media reports said the provincial chief of the Ahl-e-Sunnat Wal Jamaat, a front for the banned Sipah-e-Sahaba, had also been detained.