The "innumerable sacrifices" of Pakistan's people and security forces in the counter-terror campaign "cannot be belittled", Foreign Office spokesman Abdul Basit said.
"The leaks are an unacceptable insult to the sacrifices of our people and security forces," he said.
In a brief statement, Basit said the Pakistan government had taken "serious exception to the malicious campaign launched by certain quarters to tarnish the standing and image of Pakistani state institutions, including the security forces and the ISI".
The "baseless reports by some low-level and biased operatives" that were publicised by WikiLeaks are "misleading and evidently self-serving to justify the collective failings of the international community in Afghanistan by certain quarters", Basit said.
Pakistan has "acted in conformity with its national interests and in accordance with the principles and norms of international law and the UN charter", he said.
"We have noted that some of our close friends and partners, including the US, have been dismissive of these reports and described them as irresponsible," he added.
Pakistan had initially dismissed as "misplaced" and "skewed" the leaked US intelligence reports that accused the ISI of supporting Taliban fighters.
It also said the ongoing counter-terrorism cooperation between Pakistan and the US will continue to defeat common enemies.
The whistleblowers' website Wikileaks has made public 92,000 classified reports and cables from the US military, intelligence and civilian administration in Afghanistan.
Three publications were given access to the documents and have published a series of reports on the data.
The documents, dating from 2004 to 2009, contain allegations that the ISI was linked to a plot to assassinate Afghan President Hamid Karzai and the 2008 bombing of the Indian Embassy in Kabul.
One report said the ISI had allegedly offered 15,000 to 30,000 dollars for the killing of Indian construction workers in Afghanistan.