"The ministry has given instruction to all forces to use live ammunition to confront any assaults on institutions or the forces," the statement read.
Egypt's military-backed government also pledged in a statement to confront "terrorist actions and sabotage" allegedly carried out by Muslim Brotherhood members.
State TV blamed Morsi supporters for the arson and broadcast footage showing firefighters evacuating employees from the larger building.
The Brotherhood's website IkhwanOnLine said thousands of Morsi supporters marched through Giza but were attacked by pro-military "militias." It did not say how the government buildings were set on fire.
Attackers also set fire to churches and police stations across the country for a second day Thursday as several attempts by the Muslim Brotherhood devolved into violence.
The Brotherhood also called for protests on Friday, saying they would grow in intensity.
In the country's second largest city of Alexandria, Islamist protesters exchanged gunfire with an anti-Morsi rally, leaving scores injured, witnesses and security officials said. Attempts to storm police stations in the southern city of Assiut and northern Sinai city of el-Arish left at least six policemen dead and others injured.
Wednesday's violence started with riot police raiding and clearing out the two camps, sparking clashes there and elsewhere in the Egyptian capital and other cities.
Cairo, a city of some 18 million people, was uncharacteristically quiet Thursday, with only a fraction of its usually hectic traffic and many stores and government offices shuttered. Many people hunkered down at home for fear of more violence. Banks and the stock market were closed.
The turmoil is the latest chapter in a bitter standoff between Morsi's supporters and the interim leadership that took over the Arab world's most populous country. The military ousted Morsi after millions of Egyptians massed in the streets at the end of June to call for him to step down, accusing him of giving the Brotherhood undue influence and failing to implement vital reforms or bolster the ailing economy.