Under mounting pressure, the Internal Revenue Service and the Justice Department have announced in recent months that they will no longer use a law designed to go after drug dealers and terrorists to seize the bank accounts of small business owners who are not suspected of criminal activity. But Lyndon McLellan, the owner of a convenience store in rural Fairmont, N.C., where catfish sandwiches go for $2.75, is still trying to recover the $107,702.66 — his entire business bank account — that was seized by the I.R.S. last summer.

Under the increasingly unpopular practice of civil forfeiture, law enforcement agents can seize property suspected of having ties to crime, even if no charges are filed — and then begin forfeiture proceedings, in which the burden of proof is on the owner. Often the cost of fighting such a seizure is greater than the value of the assets seized, and law enforcement agencies get to keep forfeiture proceeds. Such a windfall, critics say, creates perverse incentives, and the lack of due process runs counter to the central tenets of the American justice system.

Mr. McLellan’s money was seized under a subset of civil forfeiture law that governs cash deposits under $10,000, the threshold at which a bank is required to report the transaction to the government. But limiting deposits to less than $10,000 to evade the reporting requirement, known as structuring, is illegal in its own right. Structuring seizures have ballooned in recent years as law enforcement task forces comb through hundreds of thousands of bank reports, often using warrants based on nothing more than a pattern of deposits. The I.R.S. alone made 639 structuring seizures in 2012, up from 114 in 2005.

The seizure dragnet has ensnared small business owners who operate with cash and may have legitimate reasons to keep their deposits low, or do not know that doing so could get them into trouble. In Michigan, for example, the owners of a drugstore had an insurance policy that only covered the loss of $10,000 or less in cash. In the case of Carole Hinders, whose modest Mexican restaurant in Iowa specialized in Insane Tacos, she was following advice dispensed by her mother decades before: that smaller deposits meant less paperwork for the bank.