Next year, for the first time, the I.R.S. will reject your tax return when filed electronically if you do not complete the information required about whether you have coverage, including whether you are exempt from the so-called individual mandate or will pay the penalty. If you file your tax return on paper, the agency said it could suspend processing of the return and delay any refund you might be owed.

The agency’s new guidance for tax professionals seems to contradict Mr. Trump’s first executive order, on Inauguration Day, which broadly instructed various agencies to scale back the regulatory reach of the federal health care law.