The online whistle-blower WikiLeaks posted the documents on its website Sunday. The New York Times, London's Guardian newspaper and the German weekly Der Spiegel were given early access to the documents.
The White House condemned the document disclosure, saying it "put the lives of Americans and our partners at risk."
The leaked records include detailed descriptions of raids carried out by a secretive U.S. special operations unit called Task Force 373 against what U.S. officials considered high-value insurgent and terrorist targets. Some of the raids resulted in unintended killings of Afghan civilians, according to the documentation.
Among those listed as being killed by the secretive unit was Shah Agha, described by the Guardian as an intelligence officer for an IED cell, who was killed with four other men in June 2009. Another was a Libyan fighter, Abu Laith al-Libi, described in the documents as a senior al-Qaida military commander. Al-Libi was said to be based across the border in Mir Ali, Pakistan, and was running al-Qaida training camps in North Waziristan, a region along the Afghan border where U.S. officials have said numerous senior al-Qaida leaders were believed to be hiding.
The operation against al-Libi, in June 2007, resulted in a death tally that one U.S. military document said include six enemy fighters and seven noncombatants - all children.
The Guardian reported that more than 2,000 senior figures from the Taliban and al-Qaida are on a "kill or capture" list, known as JPEL, the Joint Prioritized Effects List. It was from this list that Task Force 373 selected its targets.
The New York Times said the documents - including classified cables and assessments between military officers and diplomats - also describe U.S. fears that ally Pakistan's intelligence service was actually aiding the Afghan insurgency.
According to the Times, the documents suggest Pakistan "allows representatives of its spy service to meet directly with the Taliban in secret strategy sessions to organize networks of militant groups that fight against American soldiers in Afghanistan, and even hatch plots to assassinate Afghan leaders."
The Guardian, however, interpreted the documents differently, saying they "fail to provide a convincing smoking gun" for complicity between the Pakistan intelligence services and the Taliban.
In a statement released Sunday, White House national security adviser Gen. Jim Jones lauded a deeper partnership between the U.S. and Pakistan, saying, "Counterterrorism cooperation has led to significant blows against al-Qaida's leadership." Still, he called on Pakistan to continue its "strategic shift against insurgent groups."
Pakistan's Ambassador to the U.S. Husain Haqqani said the documents "do not reflect the current on-ground realities." The United States, Afghanistan and Pakistan are "jointly endeavoring to defeat al-Qaida and its Taliban allies militarily and politically," he added.
Der Spiegel, meanwhile, reported that the records show Afghan security officers as helpless victims of Taliban attacks.
The magazine said the documents show a growing threat in the north, where German troops are stationed.
The classified documents are largely what's called "raw intelligence" - reports from junior officers in the field that analysts use to advise policymakers, rather than any high-level government documents that state U.S. government policy.
While the documents provide a glimpse of a world the public rarely sees, the overall picture they portray is already familiar to most Americans. U.S. officials have already publicly denounced Pakistani officials' cooperation with some insurgents, like the Haqqani network in Pakistan's tribal areas.
The success of U.S. special operating forces teams at taking out Taliban targets has been publicly lauded by U.S. military and intelligence officials. And just-resigned Gen. Stanley McChrystal, who was leading the Afghan war effort, made protecting Afghan civilians one of the hallmarks of his command, complaining that too many Afghans had been accidentally killed by Western firepower.
WikiLeaks said the leaked documents "do not generally cover top-secret operations." The site also reported that it had "delayed the release of some 15,000 reports" as part of what it called "a harm minimization process demanded by our source," but said it may release the other documents after further review.
Jones, the White House adviser, took pains to point out that the documents describe a period from January 2004 to December 2009, mostly during the administration of President George W. Bush.
That was before "President Obama announced a new strategy with a substantial increase in resources for Afghanistan, and increased focus on al-Qaida and Taliban safe havens in Pakistan, precisely because of the grave situation that had developed over several years," Jones said.
But Sen. John Kerry, D-Mass., chairman of the Senate Foreign Relations Committee, said, "However illegally these documents came to light, they raise serious questions about the reality of America's policy toward Pakistan and Afghanistan."
A different U.S. official said the Obama administration had already told Pakistani and Afghan officials what to expect from the document release, in order to head off some of the more embarrassing revelations.
Another U.S. official said it may take days to comb through all the documents to see what they mean to the U.S. war effort and determine their potential damage to national security. That official added that the U.S. isn't certain who leaked the documents.
Another official said teams of analysts started examining the documents the moment they were disclosed online.
All three officials spoke on condition of anonymity to comment on the release of classified material.
U.S. government agencies have been bracing for the release of thousands more classified documents since the leak of a classified helicopter cockpit video of a 2007 firefight in Baghdad. That leak was blamed on a U.S. Army intelligence analyst working in Iraq.
Spc. Bradley Manning, 22, of Potomac, Md., was arrested in Iraq and charged earlier this month with multiple counts of mishandling and leaking classified data, after a former hacker turned him in.
Manning had bragged to the hacker, Adrian Lamo, that he had downloaded 260,000 classified or sensitive State Department cables and transmitted them by computer to the website Wikileaks.org.
Lamo turned Manning in to U.S. authorities, saying he couldn't live with the thought that those released documents might get someone killed.
Associated Press writers Kirsten Grieshaber in Berlin and Robert Burns in Washington contributed to this report.