The authorities on Thursday slapped a curfew in the town of Skardu where the latest violence broke out and reinforced a similar six-day-old restriction in the northern tourist destination of Gilgit.
Police across the country were placed on high alert after the death of Agha Ziauddin, who was shot in Gilgit last Saturday, sparking a weekend of unrest in which 15 people died and 35 were wounded.
Shia leaders have called for nationwide rallies on Friday to press the government to arrest the killers of the 45-year-old prayer leader, while small protests also erupted in Islamabad, Lahore and Rawalpindi, police and witnesses said.
One of Ziauddin's bodyguards who was injured in the attack also died on Thursday. Two other guards were killed instantly.
Pakistan has been plagued by sectarian violence, resulting in the deaths of more than 4000 people during the last decade.
In Skardu, some 120km from Gilgit, local officials said protesters burned down a Sunni Muslim seminary and wrecked a Pakistan International Airlines office.
Gilgit has been under a shoot-on-sight curfew since Saturday.
Local Shia leader Shaikh Mirza Ali appealed to the local people to remain calm and allow Ziauddin to receive his last rites peacefully.
"Security has been geared up across the country and police have been placed on high alert to ensure peace," interior ministry spokesman Brigadier Javed Cheema said.
Ziauddin, the leader of the Shia Anjuman-e-Imamia party, was prayer leader of the central mosque in Gilgit for the past 15 years.