After doing business this way for nearly four decades, Ms. Hinders was told that the I.R.S. had seized $33,000 from her bank account after agents detected a pattern of deposits under $10,000. Under a law designed to catch terrorists, money launderers and drug lords, depositing less than $10,000 is illegal if it is done to evade a federal bank reporting requirement, but Ms. Hinders, 67, said she never knew about the requirement.

Critics say the I.R.S. rarely investigates such cases to see if the business owner has legitimate reasons for making small deposits, such as an insurance policy that covers only a limited amount of cash.

Seizing assets without criminal charges is legal under a controversial body of law that allows law enforcement agents to seize cars, cash and other valuables they believe are tied to criminal activity. The burden of proof falls on owners seeking the return of their property. This week, the two high-ranking members on the House Ways and Means committee filed bipartisan legislation to curb abuses of the practice, known as civil asset forfeiture. Civil forfeiture has become an issue in the confirmation of President Obama’s nominee for attorney general, Loretta Lynch, who as United States attorney for the Eastern District of New York presided over a case involving more than $440,000 seized from a family-run business on Long Island.

The I.R.S. recently announced that it was sharply curtailing seizures in cases like Ms. Hinders’s, where there is no suspicion that the money involved came from an illegal source. But officials said they would not drop cases that were already underway.

Mr. Salzman said that early last week, he agreed to halt depositions in Ms. Hinders’s case when prosecutors said they would drop it, return her money, and clear the way for her to recover interest, expenses and legal fees. He wanted a “stipulated” dismissal, signed by both parties, but was unable to reach an agreement with prosecutors to include language that would declare Ms. Hinders innocent.