Most wellness plan incentives — except for that old standard, smoking cessation — won't count towards the IRS's determination of whether an employee has been offered "affordable coverage" as defined by the Patient Protection and Affordable Care Act.

The agency's stance – the final iteration of preliminary regulations generated in response to Obamacare – puts the IRS squarely at odds with wellness plan advocates.

The IRS is charged with calculating whether an employee can reasonably afford the health plan offered at work. An "unaffordable" premium is defined under the law as greater than 8 percent of household income. One factor that the IRS was willing to consider in its affordability equation was whether an employee received an incentive, in the form of a premium deduction or "bonus," for taking advantage of a tobacco cessation program. That amount would be subtracted from the company plan premium in determining affordability. In other words, it would help more employees qualify for the company plan and avoid the penalty.