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Federal prosecutors are trying to thwart the easy access that predatory lenders and dubious online merchants have to Americans’ bank accounts by going after banks that fail to meet their obligations as gatekeepers to the United States financial system.

The Justice Department is weighing civil and criminal actions against dozens of banks, sending out subpoenas to more than 50 payment processors and the banks that do business with them, according to government officials.

In the new initiative, called “Operation Choke Point,” the agency is scrutinizing banks both big and small over whether they, in exchange for handsome fees, enable businesses to illegally siphon billions of dollars from consumers’ checking accounts, according to state and federal officials briefed on the investigation.

The critical role played by banks largely plays out in the shadows because they typically do not deal directly with the Internet merchants. What they do is provide banking services to third-party payment processors, financial middlemen that, in turn, handle payments for their merchant customers.

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Yet the crackdown has already come under fire from congressional lawmakers, including Representative Darrell Issa, the Republican from California who heads the House Oversight Committee, who have accused the Justice Department of trying to covertly quash the payday lending industry.

In the first action under Operation Choke Point, Justice Department officials brought a lawsuit this month against Four Oaks Bank of Four Oaks, N.C., accusing the bank of being “deliberately ignorant” that it was processing payments on behalf of unscrupulous merchants — including payday lenders and a Ponzi scheme. As a result, prosecutors say, the bank enabled the companies to illegally withdraw more than $2.4 billion from the checking accounts of customers across the country.

The lawsuit, which includes reams of internal bank documents, offers the most vivid look yet at how some senior bank executives brushed off warning signs of fraud while collecting hundreds of thousands of dollars in fees. While the bank has reached a tentative $1.2 million settlement with federal prosecutors, the impact of the lawsuit extends far beyond Four Oaks, and federal prosecutors say this points to a problem rippling fast across the banking industry.

Banks are required under the Bank Secrecy Act, a federal law that requires banks to maintain internal checks against money laundering, to thwart suspicious activity by thoroughly examining both their customers and the companies their customers do business with. But until recently, they have largely escaped scrutiny for their role providing financial services to the payment processors.

The new, more rigorous oversight could have a chilling effect on Internet payday lenders, which have migrated from storefronts to websites where they offer short-term loans at interest rates that often exceed 500 percent annually. As a growing number of states enact interest rate caps that effectively ban the loans, the lenders increasingly depend on the banks for their survival. With the banks’ help, the lenders that typically work with a third-party payment processor that has an account at the banks are able, authorities say, to automatically deduct payments from customers’ checking accounts even in states where the loans are illegal.

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Short-term lenders argue that the loans, when used responsibly, can provide vital credit for a whole swath of borrowers largely frozen out of the traditional banking services, while state law enforcement officials say that the lenders still have to abide by state restrictions aimed at shielding residents.

And the payday industry has its defenders. Representative Issa has begun an investigation into Operation Choke Point, according to a letter addressed to Attorney General Eric H. Holder Jr.

In the January letter — a copy of which was reviewed by The New York Times — Mr. Issa accused the Justice Department of trying to “eliminate legal financial services to which the department objects.”

So far, it is unclear whether those objections will be enough to stifle the Justice Department’s investigation. But the assistant United States attorney who led the investigation is scheduled to leave the investigations in February, according to several people with direct knowledge of the matter, and the Justice Department is not extending his detail. Other lawyers within the agency are working on separate investigations related to Choke Point. The Justice Department declined to comment on the investigation, but people with knowledge of the matter say that the agency is fully committed to the project.

Some victims of unscrupulous payday lenders are pointing fingers at banks, arguing that without the aid of Four Oaks and banks like it, they never would have been plunged deep into debt by the costly loans.

James Dillon of Trinity, N.C., contends that payday lenders ransacked his checking account at Wells Fargo. A handful of the loans that Mr. Dillon, 36, took out to buy Christmas presents for his children in 2012 and 2013 — some with interest rates beyond 1000 percent — came from lenders routing payments through Four Oaks, according to a copy of his bank statements reviewed by The Times.

“Without the access from the banks, it would be nearly impossible for these lenders to operate outside the U.S. regulatory system,” said Stephen Six, a former Kansas attorney general who is part of a team of lawyers representing Mr. Dillon and other plaintiffs in lawsuits against banks over their role in processing transactions on behalf of payday lenders.

Within Four Oaks, some executives started to suspect early on that many online lenders were extending expensive credit without being licensed in the states where borrowers lived, according to the internal emails and other documents filed in connection with the lawsuit against the bank.

Bankers shrugged off evidence, even direct warnings from law enforcement officials, that their lender clients were violating state law, prosecutors say. In December 2012, for example, Arkansas’s attorney general, Dustin McDaniel, sent a letter to Four Oaks and a payday lender routing payments through the bank, accusing the company of illegally making loans to residents in his state.

The Arkansas attorney general was not the only one complaining. Between January 2011 and August 2012, Four Oaks received hundreds of complaints from banks across the country whose customers said they had never authorized merchants to withdraw money from their accounts, court records show.

Such high rates of return — the percentage of total payments returned because of lack of authorization or insufficient funds — stood out. In 2012, more than half of the payments that one Internet merchant was routing through Four Oaks were returned, a rate more than 40 times the industry standard.

The motive for tolerating such high returns, prosecutors say, was clear: outsize profits. The more questionable the merchant, the greater fees Four Oaks stood to collect, prosecutors say.

Every time consumers spot an unauthorized withdrawal and request money back, the bank makes money to process the return. And fees for processing returns, according to prosecutors, can dwarf the fees Four Oaks earned for processing the original withdrawals.

Still, the high return rates did trouble some bank executives. The problem, one banker explained in an email, was that such staggering rates imply “we don’t know our customers and we don’t do due diligence and risk grade them properly.”

Yet the bank chose to keep handling transactions for the lender, court records show.

While examining another company, Rex Ventures, bankers at Four Oaks learned that one of the investment firm’s top executives was using a false Social Security number and that an address for the company’s headquarters turned out to be a “vacant lot,” court documents show.

Still, that was not enough to dissuade Four Oaks from allowing Rex Ventures to process payments through its accounts. By August 2012, the Securities and Exchange Commission shut down Rex Ventures, accusing the company of duping investors out of $600 million.

In an email included in the lawsuit, one executive said: “I’m not sure ‘don’t ask, don’t tell’ is going to be a reasonable defense, if a state comes after one of our originators.”