As Republicans and the Trump administration continue trying to chip away at the Affordable Care Act, the Internal Revenue Service has begun, for the first time, to enforce one of the law’s most polarizing provisions: the employer mandate.

Thousands of businesses — many of them small or midsize — will soon receive a letter saying that they owe the government money because they failed to offer their workers qualifying health insurance. The first round of notices, which the I.R.S. began sending late last month, are being mailed to companies that have at least 100 full-time employees and ran afoul of the law in 2015, the year that the mandate took effect.

Large companies, defined in the law as those with 50 or more workers, are required to offer their employees affordable insurance or pay stiff tax penalties. The I.R.S. held off for years on assessing those fines, saying that it needed more time, and money, to build its compliance systems.

Now, the agency says it is finally ready to go after scofflaws.

“As the I.R.S. has publicly stated, the agency is obligated to enforce the Affordable Care Act’s employer shared responsibility provision,” said Bruce Friedland, an agency spokesman.