Jeff Swensen for The New York Times J.C. Ciesielski, 34, prepared his taxes with Richard Matthews, an accountant at Just Harvest Tax Center, in Pittsburgh this month. Mr. Ciesielski had to repay part of his health care subsidy after not adjusting his income.

PITTSBURGH When he signed up for health insurance through the Affordable Care Act last fall, J. C. Ciesielski estimated his income at $19,400, qualifying him for a federal subsidy that cut his premiums in half. But Mr. Ciesielski, an actor, earned an extra $2,340 from a voice-over job in December, and that welcome bit of income proved problematic when he did his taxes this month.

A tax preparer told Mr. Ciesielski that because he had not informed the federal health insurance marketplace, HealthCare.gov, of his additional income, he had to repay $118 of his subsidy. Mr. Ciesielski, who is being treated for a brain tumor, looked perplexed as he learned the money would come out of his refund check.

This is definitely the lowest refund Ive ever gotten, Mr. Ciesielski, 34, said as he drummed his fingers on the tax preparers desk. But it boils down to I have health insurance, which I desperately need.

This filing season, for the first time, millions of Americans are facing tax implications and new forms that even seasoned preparers are finding confusing related to their health insurance status. The changes are not only complicating things for tax filers, but also costing many of them money.

Under the Affordable Care Act, people who remained uninsured last year must either pay a penalty with their taxes, one of the most contentious elements of the law, or claim an exemption. The Obama administration has said up to six million people would owe a penalty of $95 or 1 percent of their household income, whichever is greater. But as many as 30 million people are getting exemptions, mainly because they are too poor to afford health insurance or because they live in a state that refused to expand Medicaid last year under the health law.

And people who did get insurance but, like Mr. Ciesielski, underestimated their income for 2014 the figure on which subsidies are calculated are being required to pay back part of their subsidy.

In late February, H & R Block reported that its uninsured clients had paid an average penalty of $172. The money comes out of refunds, while people who do not get refunds are required to pay the Internal Revenue Service by April 15.

The health law prohibits the I.R.S. from imposing criminal fines or putting liens on the property of people who ignore the insurance mandate, but it does allow the agency to collect the penalty by reducing future refunds.

It will still be on their books, said Courtenay Murphy, a tax preparer in Gunnison, Colo.

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Under Health Care Act, Tax Filers Find Costly Complications