Power supply to Parliament Lodges and the official residence of the Chief Justice was also ordered to be disconnected.
Minister of State for Water and Power Abid Sher Ali issued the order and said electricity connections to all institutions and individual consumers who have not paid their bills will be disconnected.
"I have issued orders that the electricity supply to Parliament Lodges, Parliament House and President's Secretariat should be disconnected immediately for non-payment of millions of rupees of bills," he said.
Giving details of the dues owed to the Islamabad Electric Supply Company (IESCO), the Minister told reporters that the Prime Minister's Secretariat owed Rs 6.2 million in dues whereas the residence of the Chief Justice of Pakistan owed a bill of Rs 1.1 million.
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He said the Capital Development Authority, Islamabad's civic agency which is responsible for paying government offices' bills, owed Rs 360 million while the Parliament Lodges owed Rs 200 million to the IESCO.
He stressed that those who will be protesting against power cuts are those whose connections have been cut due to theft.
People in some Pakistani cities are facing 10-12 hours of load shedding and the situation is expected to worsen with rising temperatures in June and July, sending demand for electricity soaring and leaving a shortfall of around 4,000 MW.
Ali said electricity theft amounting to Rs 70 billion had taken place in Balochistan where 16,000 illegal tube well connections existed.
He added that people who disconnect electricity illegally can be arrested.
The Chief Minister also said that the provincial government was ready to pay the dues of the people who could not pay their bills.