Critics say the accounts encourage overconsumption of medical services. Since consumers typically must forfeit unused money by year's end, they often ended up scrambling in December to drain their funds by loading up on aspirin, antacid and the like.

"The entire flexible spending account thing is a waste of our taxpayer dollars," says Jonathan Gruber, an economics professor at the Massachusetts Institute of Technology and a former paid consultant on the health law to the Department of Health and Human Services. "If you're going to scale it back, this is a natural place to start." (Another part of the law limits the amount consumers can save in flexible spending accounts to $2,500 a year, starting in 2013.)

Peeling back tax breaks for health plans was on the table in 2009 when lawmakers began drafting the health overhaul. Inside the Senate Finance Committee, aides to three Democratic and three Republican senators hashed out the blueprint for what ultimately became the final bill.

Compromise not 'ideal'

Some big ideas -- like limiting the tax break for employer-sponsored health insurance -- lacked support, so committee aides lowered their sights. Making people pay the full price for over-the-counter medicines seemed like a way to reduce wasteful spending and generate money for the law's main goal: expanding health insurance to nearly every American.

An objection came from William Pewen, a senior health-policy adviser to Sen. Olympia Snowe, R-Maine.

He believed the tax-free treatment could lower health costs and thought everyone should have access to a flexible spending account. He told the group that he was taking over-the-counter Prilosec, a heartburn medication, which meant he didn't need a more expensive prescription drug.

"I didn't want to see us set up perverse incentives for people to use more costly drugs than they needed," Pewen says.

He proposed a compromise that he concedes "was not the ideal solution." People could spend tax-free dollars on over-the-counter drugs, but only if they got a doctor's prescription. It wasn't exactly a new idea: Medicaid, the federal-state program for the poor, already covers some over-the-counter drugs if they are prescribed.

Congress' number-crunchers estimated the change would generate $5 billion over a decade. Hardly anyone noticed it, even as it stayed in the bill through passage in March 2010.

Only after the president's signature was dry did the American Medical Association realize what had happened and send a letter to the government warning of unintended consequences, including more office visits and extra paperwork.

Extra burden for doctors

Sure enough, when the change took effect Jan. 1, patients began bringing lists of over-the-counter drugs to office visits and also requesting over-the-counter prescriptions by phone, doctors says.

While it may not be worth the trouble for some patients, the savings can add up for those with chronic conditions, especially if the doctor writes multiple refills. A survey late last year by Nielsen found that nearly half of consumers with flexible-spending accounts would request the prescriptions as a result of the changes.

Among those most upset by the changes are pediatricians, who say that small sizes of children's medicines and multiple children per family make the requests particularly burdensome.

"It's an amazingly disruptive policy," says Dr. Jesse Hackell, a Pomona, N.Y., pediatrician who is charging $5 to fill such requests via phone. "I am now doing the IRS' work, and that's what I resent most."

After writing two over-the-counter prescriptions free of charge in January, Dr. Richard Schwartz of Vienna, Va., a pediatrician, began imposing a $10 surcharge for each prescription, on top of the office co-payment. That is likely to discourage some patients from asking for a prescription, as the surcharge could outweigh the tax savings from using a flexible spending account.

Doctors are also concerned about malpractice lawsuits, since a prescription potentially puts them on the hook for any problems a patient suffers from over-the-counter drugs.

Some malpractice insurers are urging doctors not to write any prescription without seeing the patient in person, says Lawrence Smarr, the president of the Physician Insurers Association of America, which represents malpractice insurance providers.

Drugstores caught flat-footed

Retailers and pharmacies, meanwhile, say another aspect of the change caught them flat-footed. Many flexible spending accounts come with a debit card, making it easy for consumers to draw down the money in the accounts when they shop at a pharmacy. But under the original IRS guidance, people couldn't use those cards for the prescribed over-the-counter medications.

An industry group representing Wal-Mart, CVS Caremark, Visa and other large corporations warned that could temporarily halt use of the debit cards for any pharmacy purchase. The IRS eventually decided the cards could be used, as long as the pharmacist labels and processes the over-the-counter item exactly like a prescription.

That had another unintended effect. Thousands of over-the-counter products now must pass behind the pharmacist's counter when the customer pays with the special debit card.

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"At the moment it's considered a prescription, it's subject to all the regulatory requirements," says Mike DeAngelis, a spokesman for CVS. "It runs through our quality assurance process. We have to generate a label." The chain also puts each of the prescribed drugs in an individual paper bag.

Despite the hopes of Pewen in the Senate, some consumers think they will be better off getting a prescription-only drug in place of an over-the-counter medication.

In the Nielsen survey, 37% of flexible spending account users said they would ask their doctor about prescription drugs that could replace their over-the-counter medicines.

Chung, the pediatrician in Fairfax, Va., says she recently imposed a policy under which her office writes prescriptions only for chronic conditions, like allergies. That deflects pleas from parents wanting a quick Rx for their child's cold, but she's worried about pushback. "It makes us look like the bad guy," she says.

This article was reported by Janet Adamy for The Wall Street Journal.