The hackers left messages praising India and its armed forces on the websites.
The Pakistani government is yet to comment on the matter even as the websites remain defaced.
This happens as the Islamic republic celebrates its 70th year of independence.
In 1947, The Indian Independence Act 1947 (10 & 11 Geo 6 c. 30) passed by the Parliament of the United Kingdom divided British India (a colonial territory of ancient Britain) into the two new independent dominions; the Dominion of India (later to become the Republic of India) and the Dominion of Pakistan (later to become the Islamic Republic of Pakistan).
The act provided a mechanism for division of the Bengal and Punjab provinces between the two nations, establishment of the office of the Governor-General, conferral of complete legislative authority upon the respective Constituent Assemblies, and division of joint property between the two new countries.
The partition was accompanied by violent riots and mass casualties, and the displacement of nearly 15 million people due to religious violence across the subcontinent; millions of Muslim, Sikh and Hindu refugees trekked the newly drawn borders to Pakistan and India respectively in the months surrounding independence.
On 14 August 1947, the new Dominion of Pakistan (later to become the Islamic Republic of Pakistan) became independent and Muhammad Ali Jinnah was sworn in as its first governor general in Karachi.