FBI Director James Comey. A new report commissioned by Congress highlights the bureau’s post-9/11 successes and limitations. (Cliff Owen/AP)

The FBI improved its ability to fight terrorism in the years after the Sept. 11, 2001, attacks, but a new report says the bureau still faces significant challenges as it strengthens its intelligence capabilities to deal with nimble enemies.

The finding was part of an exhaustive review requested by Congress to evaluate the FBI’s response to the 9/11 Commission’s recommendations in 2004 and determine if the domestic law enforcement agency was moving quickly enough to deal with fast-moving threats.

The lengthy report, “The FBI: Protecting the Homeland in the 21st Century,” is perhaps the most detailed, public examination of the FBI’s post-9/11 capabilities, highlighting the successes and limitations of the traditional crime-fighting bureau.

The authors of the report, a year in the making, said the FBI had come a long way, improving the sharing of information and collaborating with intelligence partners. They said the progress has “undoubtedly contributed to protecting the homeland against another catastrophic terrorist attack.”

Report: The successes and limitations of the FBI’s post-9/11 capabilities

But the FBI has lagged behind in other key programs, such as analysis and the development of a deep roster of informants, the report said. The review looked at the FBI’s response to five high-profile terrorist plots since 2008 and said informants didn’t play any meaningful role.

Members of the 9/11 Review Commission said that there were warning signs in those cases, including the 2010 botched Times Square bombing and a thwarted al-Qaeda attack on New York’s subways in 2009, that the FBI should perhaps have picked up.

The commission, which includes former attorney general Ed Meese, former congressman Tim Roemer and Georgetown University professor Bruce Hoffman, also faulted the FBI in their report for not being aware of outbursts in a mosque made by one of the brothers who carried out the Boston Marathon bombing.

However, the review commission recognized that the “civil liberties sensitivities of source networks within religious institutions” make it difficult to develop informants in local communities.

Another area of concern dealt with the FBI’s ability to evolve into an organization with a “deep expertise in intelligence and national security.”

While praising the FBI’s focus on strengthening its intelligence capabilities and making them a priority, the review found that the transformation “requires faster progress and deeper execution.”

It was only last year that FBI Director James B. Comey created a new intelligence branch, headed by an executive assistant director.

In a news conference Wednesday at FBI headquarters, Comey, who took over the bureau in 2013, said the report has been “a tremendously valuable thing to me as director.”

“We want the American people to see what they are getting for their money,” said Comey, who noted about 90 percent of the report was declassified. “What the FBI is doing. What the FBI is doing well. What the FBI could do better.”

Comey said much of the progress the FBI had made was due to the efforts of his predecessor, Robert Mueller, a former Marine who began running the bureau mere days before the 9/11 attacks.

Other issues identified in the report — which Roemer said he hoped would serve as a blueprint for the FBI over the next quarter century — are the recruitment of people with the necessary skills to deal with complex missions, such as cyberthreats, and hiring linguists.

Leadership at the bureau was also examined, with the report finding “passive resistors” when it came to making necessary changes. The report said in the years ahead “visionary leadership will matter more than ever.”

The review also tackled the FBI’s relationships with other agencies such as the Department of Justice’s National Security Division. The NSD consults and in some instances approves certain FBI investigative activities.

The general perception among FBI agents and supervisors interviewed by the 9/11 Review Commission was that the “NSD works too slowly and has been insufficiently aggressive in supporting the FBI’s surveillance requests.”

One bright spot in the report: The CIA and FBI seem to be getting along better, putting aside the traditional friction that existed before the 9/11 attacks.

“The relationship between the FBI and CIA domestically and overseas appears to be on solid ground, and is arguably the strongest it has been in their collective history.”