Pentagon: Irregular report
The Washington DC-based think-thank that published the report was co-founded by Michele Flournoy, who was appointed undersecretary of defence for policy in February.
The Pentagon expressed surprise on Tuesday at the criticism, calling it an "unusual and irregular way to publish a document of this nature".
"I think it struck everybody as a little bit curious, yes ... My sense is that this was an anomaly and that we probably won't see that [in the future]," Bryan Whitman, a Pentagon spokesman, said.
Whitman did not question the substance of the report but cautioned that officials were still reviewing it.
"I think it's a candid assessment of some of the shortcomings there [in intelligence] and the challenges that face us," he said.
Intelligence agents need to ascertain a greater volume and breadth of information at a local level, according to the report, authored by Flynn and Matt Pottinger, his chief adviser.
The report, which highlighted tensions between the military and intelligence agencies, said too great a focus had been given to gathering information on opposition groups and an "anti-insurgency campaign" to capture mid and high-level opposition agents.
Consequently fundamental questions about "the environment in which US and allied forces operate and the people they seek to persuade" were left unanswered, it said.
Less than a week ago, a suspected al-Qaeda double agent from Jordan killed seven CIA agents in Afghanistan in a suicide bomb attack.
It was the second-highest loss of life the CIA has suffered in a single attack in its history.
Last month, Barack Obama, the US president, assigned a further 30,000 troops to Afghanistan, to focus on training local forces to replace American personnel in the country.
'Resources spread thin'
Richard Schoeberl, a former Federal Bureau of Investigation (FBI) counter-terrorism official, told Al Jazeera: "We're almost a decade into this war ... the problem is the right information that needs to be gathered is not being gathered or its being gathered but not disseminated properly."
Schoeberl said there were not enough analysts on the ground and those there were not in the necessary areas because the areas were too dangerous.
And the intelligence databases of the many different nations operating in Afghanistan were incompatible, according to Schoeberl.
"We've got the Jordanian database, which we don't have access to, then the UK's, the US's ... then it's separated with the FBI, the CIA," he said.
"It's hard to filter through all this information, find the right information and get to the people on the ground and to the people higher up who are actually making the decisions.
"The fact is there are not enough people to do the amount of work needed to be done. We are spread thin in the intelligence community and the armed forces to conduct the type of operation we are trying to conduct."