It is unclear who the source of the leaked documents is, and Jones did not address the veracity of the information contained in the leaks.
He did point out that the documents "reportedly cover a period of time from January 2004 to December 2009", the bulk of which time George Bush, the former US president, was in office.
Jones also noted that Barack Obama, who took over from Bush, announced on December 1, 2009 "a new strategy with a substantial increase in resources for Afghanistan, and increased focus on al- Qaeda and Taliban safe-havens in Pakistan".
"This shift in strategy addressed challenges in Afghanistan that were the subject of an exhaustive policy review last fall," Jones said.
The documents were released by the online whistle-blower Wikileaks website, which gave US newspaper The New York Times, Britain's Guardian newspaper and the German weekly Der Spiegel access earlier.
Eric Schmitt, one of the New York Times reporters who worked on the story, 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".
They painted "a much grimmer picture and portrayal than either the Bush or Obama administrations have allowed so far", he said.
According to the reports, the US deploys special forces to work from a capture or kill list, missions that were stepped up under the Obama administration and that have led to some civilian deaths.
Also, the US has tried to cover up the fact that the Taliban have heat seeking surface to air missiles.
And the documents say the CIA expanded paramilitary operations in Afghanistan and ran the Afghan spy agency from 2001-2008.
Worries over Pakistan
The documents also describe US fears that ally Pakistan's intelligence service was aiding the Taliban.
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 organise networks of militant groups that fight against American soldiers in Afghanistan, and even hatch plots to assassinate Afghan leaders".
That prompted Pakistan's ambassador to the US to denounce the leak and insist his nation was fully committed to fighting al-Qaeda and the Taliban.
Husain Haqqani 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 onground realities," Haqqani said in a statement.
|The reports say the Taliban has heat seeking surface to air missiles [Reuters]
"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.
Pakistan's Inter-Services Intelligence (ISI) agency helped establish the Taliban's government in the 1990s, when Afghanistan was wracked by infighting following the withdrawal of Soviet troops.
Pakistan'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.
Last year, Robert Gates, the US defence secretary, said "the ISI's contacts with [extremist groups] are a real concern to us, and we have made these concerns known directly to the Pakistanis".
Ambassador Haqqani said the latest reports of the leaked documents "reflect nothing more than single-source comments and rumours, which abound on both sides of the Pakistan-Afghanistan border and are often proved wrong after deeper examination".
Wikileaks is one of the internet's biggest sources of classified government information.
In April, it 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 risk for allegedly leaking a the classified video.
More deaths expected
The leaked documents come as the top US military officer said on Sunday that more Nato troops will die in Afghanistan as violence mounts over the summer.
Admiral Mike Mullen, the chairman of the joint chiefs of staff, said on a visit to Afghanistan, however, that Washington's goal of turning the tide against the Taliban by year's end was within reach.
Violence in Afghanistan is at its highest of the 9-year war as thousands of extra US troops, dispatched by Obama in December, step up their campaign to drive Taliban fighters out of their traditional heartland in the south.
Last month was the deadliest for foreign troops since 2001, with more than 100 killed, and civilian deaths have also risen as ordinary Afghans are increasingly caught in the crossfire.
"As we continue our force levels and our operations over the summer ... we will likely see further tough casualties and levels of violence," Mullen told a news conference in Kabul.
Despite the rise in casualties, Mullen said "slow but steady" progress was being made and that Washington's strategy of reversing the Taliban's momentum was still obtainable by the end of the year.
The next months would be crucial, he added.
"No one is declaring victory but there is progress," he said. "I believe that goal is still achievable and certainly the proof of that will be what happens over these next many months in what is a very challenging period."