CHICAGO — The report to Congress was blunt: The Environmental Protection Agency had failed to regulate pollution from the nation’s livestock farms — many capable of generating more waste than some cities — because it lacked information as basic as how many farms even existed.

Four years after the US Government Accountability Office raised concerns and 40 years after the Clean Water Act gave the EPA the authority to protect the nation’s waterways, the agency still doesn’t know the location of many livestock farms, let alone how much manure they generate or how the waste is handled, because most of that information is kept by various state and/or local agencies — or not collected at all.

At the same time, water-quality specialists cite livestock waste as a major contributor to water-quality problems, including in areas like the Chesapeake Bay, where manure runoff is believed responsible for up to one-fourth of phosphorus, which stimulates algae growth. If the EPA knew all the sources of that waste, it might be easier to stop it, environmentalists say.

So they were flabbergasted when the EPA recently decided against adopting a rule that would require livestock operators to provide the agency with information, opting instead to try to cobble it together from other state, local, and federal sources.

‘‘It’s been [decades] since we first started regulating them and we’re not at a point where we know where they’re at?’’ said Kelly Foster, senior attorney at Waterkeeper Alliance, one of several environmental groups that sued the EPA to get it to start collecting information on concentrated animal feeding operations.

It’s not unusual for these operations to have thousands of cattle, tens of thousands of hogs, or millions of chickens in one location. Pollution from faulty manure storage or runoff happens often enough to generate complaints, and environmentalists suspect many more problems go undetected.

To settle Waterkeeper’s lawsuit, the EPA agreed to propose the rule requiring livestock operations to report information to the agency. But it didn’t promise to adopt it.

Industry officials said there’s no reason for farmers to have to give the EPA information, especially if another government agency already has it or a farm isn’t doing anything wrong.

‘‘We’re not keeping them from getting the information, but we don’t need to turn it all over,’’ said Michael Formica, an environmental lawyer for the National Pork Producers Council, which threatened to sue if the rule was adopted.

EPA spokeswoman Cathy Milbourn said nobody was available to discuss the decision. But the agency issued a statement saying it was withdrawing the proposed rule ‘‘in light of comments received from states regarding the amount of information states already have.’’

The EPA signed an agreement with the Association of Clean Water Administrators, whose members include state water-quality officials, to have that group help identify where the information is kept and how the EPA could get it. Alexandra Dunn, executive director and general counsel of the association, said her group believes it’s better to assess how much information is already available before requiring farmers to report it, but she acknowledged the EPA will be able to get only the information other agencies are willing to share.

It’s unclear how that would play out in some Republican-led states, where officials have been increasingly critical of EPA efforts to regulate everything from greenhouse gases to gas drilling. Even in states like Illinois, getting information may be difficult.

The Illinois agriculture department approves farm construction and informs the state EPA, but even agriculture officials don’t know where all of Illinois’s livestock farms are located because many were built before the state began requiring preapproval in 1996.