Billions of dollars were pumped into counter-terrorism and other intelligence work following the September 11 attacks, but because of the clandestine nature of the agencies involved, until now it has not been clear how the money was being spent.
The newspaper found that there were nearly 1,300 government organisations tasked with intelligence work - and quoted senior officials admitting that the sprawling network was difficult to co-ordinate effectively.
"There has been so much growth since 9/11 that getting your arms around that - not just for the DNI [Director of National Intelligence], but for any individual, for the director of the CIA, for the secretary of defence - is a challenge," Robert Gates, the US defence secretary, told the newspaper.
Complexity 'defies description'
John Vines, a retired army lieutenant-general who was tasked last year with reviewing the Pentagon's top secret programmes, said the "complexity of this system defies description".
Vines said in an interview with the Post, he was "not aware of any agency with the authority, responsibility or a process in place to co-ordinate all these interagency and commercial activities".
"You can get so much intelligence that you can't actually see the forest for the trees"
former CIA field agent
The investigation reveals that almost one million Americans are cleared to top-secret level, and that intelligence and national security work takes place in some 10,000 locations across the country.
The intelligence community in the US produces almost 150 reports a day; so many that the newspaper says "many are routinely ignored".
Jack Rice, a former CIA field agent, told Al Jazeera that following the September 11 attacks there was an attitude that "more is better" in the intelligence services.
"That's not always true. You can get so much intelligence that you can't actually see the forest for the trees," he said.
"There's so much that you can't actually pick out the importnant pieces, which by the way, is actually the same problem as on 9/11 ... it is the same problem that we have had again and again and again. It continues regardless of how big we are and sometimes it gets worse the bigger we get."
After the article's publication, intelligence officials in the US hit back at the claims, saying that the newspaper had not given a fair reflection of the important work carried out by the services in question.
Al Jazeera's Rosalind Jordan reports on the myriad of intelligence agencies in the US
David C Gompert, the acting director of national intelligence, issued a statement criticising the Washington Post.
"The reporting does not reflect the intelligence community we know," he said.
"We accept that we operate in an environment that limits the amount of information we can share.
"However, the fact is, the men and women of the intelligence community have improved our operations, thwarted attacks, and are achieving untold successes every day."
But Pete Hoekstra, the senior opposition Republican on the House of Representatives intelligence committee, said the Washington Post account confirmed "the national security bureaucracy is large, redundant and lacks the nimbleness to respond to threats posed to our nation".
He said it was "frustrating" that, years after the US Congress cast a critical eye on US intelligence efforts after the 9/11 attacks, problems had still gone unanswered.
The report also showed the degree to which US intelligence gathering and analysis has been farmed out to private contractors, with 1,931 private companies said to be working on counter-terrorism related programmes.
Ray McGovern, a former CIA analyst, told Al Jazeera that the use of private companies could cause a conflict of interest.
"It's privatisation run amok," he said.
"To get their contracts renewed for the following year they will hue, they will dodge and they will dance around to give the right answer."
He warned that the sheer size of the intelligence community may undermine the work it is trying to do. "If you are trying to find a needle, the way to do that is not to add more hay to the stack," he said.
The Washington Post said it had based its investigation on government documents, job descriptions, property records and hundreds of interviews with officials familiar with different parts of the intelligence gathering network.