Perhaps the most troubling aspect of the reports for U.S. officials are those which strongly suggest the ISI was double crossing the U.S. Last year, a report suggested that the former head of ISI was encouraging insurgents to focus their operations in Afghanistan "in exchange for the government of Pakistan's security forces turning a blind eye" to insurgents in Pakistan.
"While we and others have reported on this in broad themes over the past couple of years, the reports are voluminous. Even if you toss out ones that are perhaps disinformation or the bias of the Afghan intelligence service, they are generally consistent with other classified reporting by American intelligence analysts that the ISI still does have connections with many of these groups that are conducting attacks in Afghanistan," Schmidt said.
Speaking on the condition on anonymity, a senior ISI official told ABC News today the documents amounted to "the usual rhetoric and nothing new.
"It seems to be all rubbish and maybe not worth commenting," the official said, emphasizing that the agency was still shifting through the documents.
In response to the leak, White House issued a statement from National Security advisor Gen. James Jones condemning the "disclosure" which "could put the lives of Americans and our partners at risk" but saying their release will not change America's course in the region.
"These irresponsible leaks will not impact our ongoing commitment to deepen our partnerships with Afghanistan and Pakistan; to defeat our common enemies; and to support the aspirations of the Afghan and Pakistani people," Jones said in the statement.
Assange told the British newspaper The Guardian why he chose to make the documents public.
"In this case it will show the true nature of this war and then the public from Afghanistan and other nations can see what is really going on and can take steps to address the problems," he said.
A spokesman for Afghanistan's President Hamid Karzai said today the Afghan government has had concerns about the ISI involvement and said "measures have to be taken" for bringing the number of civilian casualties down.
Assange still has yet to release another 15,000 documents, Schmidt said. Schmidt told "Good Morning America" great effort was taken to work with the White House on the newspaper's report not to put any soldiers in harm's way.
CLICK HERE to see the New York Times' report.
ABC News' Nick Schifrin and Jim Scuitto contributed to this report.