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Two-thirds of employees pay the same price for deductibles as they did last year, but 28 percent pay more, and only four percent pay less.

Owners are also covering higher insurance premiums, with 66 percent of small businesses cutting into profits to pay for cost increases, while 40 percent delayed, postponed or eliminated business investment to make room for health insurance. Nearly half of employers also sought to increase productivity to pay for the costs.

The authors of the study say the Obama administration’s flawed rollout of the Affordable Care Act is part of the problem.

“The law’s authors were primarily focused on increasing insurance coverage and expanding benefits — they gave little or no consideration to concerns about cost or who would foot the bill,” said William J. Dennis, the author of the study and a senior fellow at the NFIB Research Foundation.

“Ironically, had they instead made reducing costs a priority, this would have been a natural incentive for increasing coverage. Unfortunately though, this single-minded approach resulted in a law with a rising price tag, and Obamacare’s authors failed to consider that someone has to pay for all the bells and whistles included in the law,” Mr. Dennis said. “That ‘someone’ it turns out is often the small-business community — small employers, their employees and their families.”

The NFIB will conduct the survey once a year for three years to track the impact of the Affordable Care Act on small businesses’ finances.

“We see the results of this year’s research as establishing a baseline; what we will learn from the developing responses in the next two years will tell us more and more about the law and how it changes — or does not change — the behaviors of the small-business community,” Mr. Dennis said.

Tim Devaney contributed to this report.