Details on the intelligence community's threat assessment was included in the White House's classified fiscal year 2013 budget for intelligence operations, handed over to the Post by Snowden.
Of the 50 top counter terrorism threats facing the United States, American intelligence agencies have made "moderate progress" on 38 of those objectives.
As part of that assessment, intelligence officials noted that lack of insight into Pyongyang's nuclear program tops the list of so-called "critical" gaps in American espionage and counterterrorism efforts.
Among the foreign nations aspiring to become nuclear powers, Washington has the least visibility into the inner workings of the North Korean program.
In April, Director of National Security James Clapper told Congress that keeping tabs on the North Korean regime has become an uphill battle for U.S. intelligence.
"I ... have to say that North Korea, of course, is now and always has been one of the, if not the toughest intelligence targets," Clapper told members of the House intelligence committee at the time.
That blind spot in U.S. intelligence operations nearly came to a head earlier this year, when provocations by North Korean dictator Kim Jong Un brought the region to the brink of war.
The game of one-upmanship between Washington and Pyongyang ended when Kim reportedly gave his military the green light to launch nuclear strikes against U.S. allies in the Pacific and targets inside the United States.
While tensions eventually subsided, the threat of attack shed a light on the intelligence community's lack of understanding into the regime.
Aside from North Korea, American intelligence has had difficulty tracking movements of Pakistan's nuclear and chemical weapons arsenal, according to the Post.
To that end, Washington is expanding efforts to collect details on Russia's chemical weapons capabilities, as well as "biological and chemical laboratories" run by Islamabad.
But, like Pyongyang's atomic weapons programs, staying abreast of Pakistan and Russia's chemical and nuclear stockpiles has also proven extremely difficult, according to the classified intelligence documents.