The sharing of crucial intelligence about counter-terrorism between the FBI, the Department of Homeland Security and local police departments takes place through a patchwork process that amounts to “organized chaos”, according to a new report.

The report, released Tuesday by the Brennan Center for Justice, a public-policy institute at New York University law school that has a track record of being skeptical of government surveillance, found inconsistent rules, inadequate oversight, apparent wastefulness and insufficient regard for civil liberties nationwide.

“This poorly organized system not only wastes time and resources; it also risks masking reliable intelligence that could be crucial to an investigation,” the report says, warning that a “din of data” is overwhelming law enforcement.

“There’s a lot of irrelevant information being collected,” said Michael Price, a counsel with the Brennan Center and the author of the report.

“As a result of that, it seems pretty easy for information to slip through the cracks.”

A Department of Homeland Security spokesman took vigorous exception to the report’s factual presentation and its conclusions, saying that much of the responsibility for the patchwork rules should properly be attributed to discrepancies in laws across the 50 states and arguing that the fusion centers contribute strongly to national security while protecting civil liberties.

Scrutiny of the wide-reaching intelligence apparatus in federal, state and local law enforcement since 9/11 has largely taken a backseat during the past six months’ worth of revelations from whistleblower Edward Snowden about the National Security Agency’s surveillance activities. But this week, several reports pointed to an enormous amount of data collected by police departments – particularly from cellular towers.

The Brennan Center report examined 16 major police departments across the US, along with 19 affiliated “fusion centers” – controversial data-sharing pools between federal, state and local agencies – and 14 of the FBI’s joint terrorism task force partnerships with police.

It found, among other problems, inconsistent quality control, which permitted a flood of local tips – some as innocuous as “ordering food at a restaurant and leav[ing] before the food arrives” (an example from California, according to a Fusion Center training document obtained by the report's authors) – into fusion centers.

Data like that does not meet the legal standard for "reasonable suspicion" normally required to pursue surveillance, let alone the requirements of probable cause. Yet it can be stored within fusion centers and accessed by a variety of law enforcement and homeland security agencies for up to a year, the report said.

Despite efforts by the Department of Homeland Security, most of the fusion centers operate with “minimal oversight, or no oversight whatsoever”, the report found. Out of 19 centers reviewed, only five require independent audits of retained data.

“We’re calling for clear, consistent processes and stronger standards for collecting and sharing information to reduce some of the noise coming from this din of data,” Price said.

A Department of Homeland Security spokesman contended Tuesday that the report misrepresented the complexities of data-sharing across local, state and federal agencies, and strongly defended the relevance and performance of fusion centers.

“This report fundamentally misunderstands the role of fusion centers within our national security structure and their value to state and local law enforcement,” said DHS press secretary Peter Boogaard.

“As pointed out by congressional leaders and major law enforcement organizations across the country, fusion centers greatly improve information sharing and co-ordination between federal, state and local law enforcement. By receiving classified and unclassified information from the federal government and assessing its local implications, fusion centers help law enforcement on the front lines better protect their communities from all threats, whether it is terrorism or other criminal activities.”

The FBI did not respond to a request for comment made after a media embargo on the Brennan Center report lifted.

Fusion centers have been the subject of criticism from both civil libertarians and powerful elected officials. A 2012 investigation by the bipartisan Senate permanent subcommittee on investigations of more than 80,000 fusion center documents could not find any contribution the centers had made to “disrupt[ing] an active terrorist plot”. DHS disputes the results of that investigation, as do several legislators on committees overseeing the department.

Senator Tom Coburn, an Oklahoman who serves as the top Republican on the Senate government reform and homeland security committee, has emerged as a leading legislative critic of fusion centers and joint terrorism task forces, for many of the same reasons detailed in the Brennan Center report. After a government inquiry indicated many federal data-sharing efforts were duplicative, Coburn issued a statement in April calling them “a vital component of national security”, but adding, “that is not an excuse to waste taxpayer funds”.

The Brennan Center’s report comes as police departments’ widespread use of cellphone data is attracting new scrutiny.

On Monday, the Washington Post revealed that police departments around the country relied 9,000 times last year on so-called “tower dumps”, or data collected from cellphone signals that went to a given cellphone tower during a certain period of time. That data necessarily includes call information from cellphone subscribers who are never suspected of any crime.

“There are serious questions about how law enforcement handles the information of innocent people swept up in these digital dragnets,” congressman Ed Markey, a Massachusetts Democrat who plans to introduce legislation limiting tower dumps, told the Post.

Also on Monday, USA Today reported that approximately a quarter of police departments in the US have employed tower dumps, and at least 25 departments around the country employ a portable piece of spoofing hardware, called a Stingray, that tricks cellphones into thinking it is a cell tower, allowing it siphon data and send it directly to police.

And all that information is on top of the fruits of the NSA’s vast data collection efforts, which are not entirely off limits to federal law enforcement. The controversial bulk collection of Americans’ phone data has been repeatedly described by the NSA as a tool to aid the FBI in detecting domestic terrorism activity.

NSA deputy director John C Inglis recently stated that the FBI cannot search directly through the NSA’s data troves, but the agency shares telephone metadata with the bureau following searches through its databases based on “reasonable articulable suspicion” of connections to specific terrorist organizations.

The Brennan Center report did not specifically analyze law enforcement tower dumps, but Price called the reports of them alarming.

“This is another indication of the vast trove of information that state and local police are collecting about law abiding Americans,” Price said. “To date, that information does not appear to be particularly useful in preventing terror attacks.”