Wikileaks' documents, which cover a period from January 2004 to December 2009, include descriptions of a covert US special operations unit formed to target high-level al-Qaeda and Taliban figures.
They say more than 2,000 leaders are on a "kill or capture" list, but missions to hunt them down have led to unreported civilian deaths.
Julian Assange, the founder of Wikileaks, said he expected the leaked records would "shape a [new] understanding of the past six years".
"The real story of this material is that it's war, it's one damn thing after another," Assange said at a news conference in London on Monday. "It is the continuous small events, the continuous death of children, insurgents, allied forces, the maimed people."
The New York Timesin the United States, Britain's Guardiannewspaper and the German weekly Der Spiegelwere all given about a month's advanced access to the dosier, with each jointly unveiling their findings on Sunday.
According to the Times report, the documents suggest Pakistan "allows representatives of its spy service to meet directly with the Talibanin secret strategy sessions to organise networks of militant groups that fight against American soldiers in Afghanistan, and even hatch plots to assassinate Afghan leaders".
Husain Haqqani, Pakistan's ambassador to the US, called the release of the files "irresponsible" and said it consisted of "unprocessed" reports from the field.
"The documents circulated by WikiLeaks do not reflect the current on-ground realities," Haqqani said in a statement.
"The United States, Afghanistan and Pakistan are strategic partners and are jointly endeavouring to defeat al-Qaeda and its Taliban allies militarily and politically," he said.
The US government also condemned the records' disclosure, saying they could threaten national security and endanger the lives of its forces.
PJ Crowley tells Al Jazeera most of the leaked documents on Wikileaks are "years old"
"The United States strongly condemns the disclosure of classified information by individuals and organisations which could put the lives of Americans and our partners at risk," James Jones, the US national security adviser, said.
"These irresponsible leaks will not impact our ongoing commitment to deepen our partnerships with Afghanistan and Pakistan; to defeat our common enemies."
Assange, however, defended his organisation's decision to release the classified files, saying Wikileaks "tried hard to make sure this material does not put innocents at harm", adding that all the documents were at least seven months old.
Rejecting US government claims, he said: "We are familiar with groups whose abuse we expose attempting to criticise the messenger, to distract from the power of the message ... we don't see any difference in the White House's response in this case to the other groups that we have exposed."
According to the records, the US has tried to cover up the fact that the Taliban have heat-seeking surface-to-air "stinger" missiles.
The documents also show that the Taliban's widening use of roadside bombs have killed more than 2,000 civilians.
Eric Schmitt, one of the New York Times reporters who worked on analysing the files over the last month, told Al Jazeera that the documents gave an unvarnished view of the war, a "very fine grain, down on the ground level detail that hasn't been revealed before ... whether it's in firefights or drone activities, secret operations performed by commandos of the CIA".
Pakistan's ex-spy chief denies allegations of active links with the Afghan Taliban
He said they painted "a much grimmer picture and portrayal than either the Bush or Obama administrations have allowed so far".
Included in the many revelations of the leaked documents were also reports that the CIA expanded paramilitary operations in Afghanistan and ran the Afghan spy agency from 2001-2008.
Pakistan's ISI had helped establish the Taliban's government in the 1990s, when Afghanistan was wracked by infighting following the withdrawal of Soviet troops.
The country's leadership reversed course after the September 11, 2001 attacks on the US, agreeing to assist the US against the Taliban, which the US accused of sheltering Osama bin Laden, the al-Qaeda leader.
But US officials and analysts have persistently questioned whether all of Pakistan's security apparatus is on the same page, with some believing that Islamabad's main interest is to ensure continued influence in Afghanistan.
Wikileaks has become one of the biggest and most controversial sources of classified government information, even publishing a document showing that US intelligence had plans to shut it down.
|The documents reveal new details about Afghan civilian deaths [EPA]
In April, Wikileaks released video footage from a helicopter cockpit showing a deadly 2007 aerial strike in the Iraqi capital that killed 12 civilians, including two journalists from the Reuters news agency.
Army Specialist Bradley Manning, 22, was charged this month with misconduct and putting national security at riskfor allegedly leaking the classified video, and has now been implicated in the release of the Afghan documents as well.
Sunday's released records consist largely of classified reports and assessments from junior officers in the field that analysts use to advise policymakers.
The leak is expected to put further pressure on Barack Obama, the US president, to get results in Afghanistan as he send thousands of additional troops to bolster forces already in the country.