One of the assailants was also killed by Ziauddin's guards, Baloch said.
Rampaging mobs set fire to several government and private buildings and also torched the home of forest officer Taighun Nabi, burning him and five members of his family to death, deputy commission Baloch said.
In another attack, local health department chief doctor Sher Wali was trapped in his office and shot by the mob, his cousin Badar Munir said.
A male passer-by was also hit and died as the mobs shot randomly in the streets, said another senior local official, Jamil Ahmed.
The city was tense as troops enforced the curfew with orders to shoot on sight anyone caught outside, residents said.
Meanwhile, Information and Broadcasting Minister Sheikh Rashid said the incident in Gilgit is an act of the enemies of Pakistan who want to create instability.
Talking to PTV, he said, unknown people tried to assassinate Agha Zia which created law and order situation and the army was called in.
"I think killing someone or destroying private property has nothing to do with Islam. Those responsible for all this are neither Muslims nor Pakistanis," he said. He termed the incident as regretful and condemned it.
He said certain elements cannot see a stable Pakistan and from time-to-time they try to create situations like this to tarnish the image of the country internationally.
He said, "We are heading forward with a positive thinking, with harmony and fraternity as a responsible nation and we have done away with the issue of sectarianism. This is our image they want to spoil." The law will take its strict course against them, he warned.