Small-business owners have accused some of the country’s largest banks of unfairly favoring applications from their wealthiest clients for aid under a $349 billion government stimulus program.

Customers of Bank of America, JPMorgan Chase and Wells Fargo have sued the banks in federal court, saying data provided by the Small Business Administration on the average size of the loans shows they doled out money to larger customers first.

The S.B.A., which is administering the stimulus program, known as the Paycheck Protection Program, designated it a first-come-first-served operation but gave banks wide latitude on whose applications to accept.

The lawsuits — two against Chase and one each against Bank of America and Wells Fargo, all filed in the Central District of California — say smaller customers were not given the chance to apply as quickly as larger ones in some cases. In other instances, the lawsuits say, the banks sat on some smaller customers’ applications instead of immediately submitting them to the S.B.A.

The program ran out of money on Thursday, leaving many small-business owners wondering how they would survive. Lawmakers are working on a deal to add $300 billion to the program.

Longstanding rules that require banks to know their customers’ backgrounds and sources of funds made it easier to take applications from existing customers rather than allow new customers access to the program. Some lenders, like Bank of America, turned away applications they received from borrowers who had gotten a loan or a credit card from another bank — a decision that a federal judge said this month was consistent with the stimulus program’s design.

However, for applications they planned to consider, the banks were supposed to handle each one as soon as it came in, not set any aside until later. The business owners who are suing say the banks did just that. Each of the lawsuits, which are seeking class-action status, claims the banks put a priority on larger loans because the banks could collect higher fees on them.

“We deny the allegations,” said Bill Halldin, a Bank of America spokesman.

The lawsuits rely heavily on two reports that the S.B.A. issued describing the types of loans it had been processing. The most recent, on Thursday, showed far more loans of $150,000 or less going through the system than a report three days earlier. This suggests, the lawsuits claim, that the banks held off on considering many smaller loan requests until they had completed the larger ones.

The S.B.A. reports do not identify banks by name. But the report on Thursday shows the largest lender, “Lender 1,” as having distributed more than $14 billion in the program. Chase released a statement a day later saying it had distributed that amount of money, more than any other lender.

According to the S.B.A.’s report, Lender 1’s average loan was $515,304, suggesting that many loans were going to businesses with short-term expenses that were “well above the needs of the average small business,” one of the lawsuits said.

Chase said on its website on Sunday that some of the disparity in speed had to do with which part of Chase’s operations the clients applied to for help. Its commercial bank, which serves larger companies than its consumer bank’s small-business banking operation does, received fewer loan requests, so it was able to process loans more quickly, Chase said.

“Within each business, we did not prioritize certain clients, large or small,” it said.

A Wells Fargo spokeswoman declined to comment on the lawsuit against it.

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