(New York Times) 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.

Ten months ago, in his first executive order, President Trump directed government agencies to waive, defer or delay carrying out as much of the law as possible. This week, the Treasury Department said that it objected to the employer mandate but was legally compelled to enforce it.

“Treasury lawyers see no ground for the secretary to direct the I.R.S. to not collect the tax,” the agency said in a written statement. “The A.C.A.’s employer mandate unfortunately remains the law of the land.”

Senate Republicans plan to include a repeal of the law’s individual mandate in their tax cut bill. Eliminating that mandate, which requires people to buy health insurance or pay a penalty, would free up hundreds of billions of dollars that could be redirected to tax cuts. The I.R.S. recently indicated that it would tighten enforcement of that provision as well.

The employer mandate, which would be unaffected by that proposed change, is lucrative for the government. It is expected to bring in penalty payments of $207 billion over the next decade, according to projections by the Congressional Budget Office.

When the health law was passed, lawmakers feared that without an employer mandate, companies would cancel their insurance benefits and send large numbers of employees to the health care law’s insurance exchanges, where many people qualify for government subsidies. Employees who are offered health insurance through their jobs are ineligible for the subsidies.

The law’s exact rules are complex, but businesses will generally incur fines of around $2,000 per employee (excluding the first 30) if they do not offer qualifying coverage to nearly all of those who work an average of 30 or more hours a week. The penalty is activated if at least one employee then buys insurance on the health law’s marketplace and receives a subsidy for it.

The per-employee fine increases each year, and can add up quickly: A company with 100 workers that ignored the law this year would owe a penalty of more than $158,000.

To prove their compliance, businesses are required to send the I.R.S. a report on their employee head count and the health care coverage that they offered. The tax agency began requiring those forms two years ago, but it repeatedly ran into problems processing them.That delayed efforts to identify, and fine, companies that did not offer their workers adequate insurance. The bottleneck largely came down to money, according to the agency.

“For the past four years, the I.R.S. has received almost no funding for implementation of the Affordable Care Act,” John A. Koskinen, then the agency’s commissioner, told Congress last year. (Mr. Koskinen’s tenure at the agency ended this month, but no change in the enforcement of the mandate is expected.)

A recent audit by the Treasury’s inspector general for tax administration found that the I.R.S. had “delayed, not initiated or canceled” crucial systems needed to enforce the employer mandate. Other systems “did not function as intended,” causing confusion both for the agency and for companies trying to comply with its reporting requirement

Accountants and others familiar with the process say they are bracing for more problems.

“Our belief is that very few of these are going to be accurate,” Roger Prince, an accountant and lawyer with the consulting firm Berry Dunn in Portland, Me., said of the penalty notification letters being sent out.

Those letters are based on the reporting forms companies submitted for 2015 — the first year that they had to complete the new, and complex, disclosures.

“Every single one we looked at for our clients was wrong,” Mr. Prince said. “We always had to send them back corrections.”

Large companies are generally taking the process in stride, trade group representatives said. They are accustomed to back-and-forth discussions with the I.R.S. over their tax bills and have teams of experts to handle complicated compliance issues.

But for smaller companies, the ones most likely to owe penalties, the mandate’s slow and messy enforcement has raised concerns. Nearly all large employers offer their employees insurance, but among companies with 50 to 199 workers, around 8 percent do not, according to the Kaiser Family Foundation’s annual employer survey.

“It’s been very obscure and confusing,” Kevin Kuhlman, the director of government relations for the National Federation of Independent Business. “The lag time is worrisome. We’re talking about penalties for 2015, and here we are almost in 2018.”

R. Pepper Crutcher Jr., a lawyer in Jackson, Miss., who works with midsize employers, said he thought many companies would be “blindsided” by the notification letters.

Even companies that fully comply with the mandate have struggled to master its complicated reporting rules, Mr. Crutcher said. And the I.R.S. has also struggled to correctly analyze the returns, the inspector general’s audit found.

The agency said companies that disagreed with its penalty notifications must contact it within 30 days to document their dispute.

But simply pleading confusion or financial hardship will not work, the agency has indicated.

Representative Bill Huizenga, a Michigan Republican, contacted the agency recently on behalf of an employer in his district that expected to owe a penalty payment. It had not complied “for both financial and religious reasons,” the employer said.

The I.R.S. said it would still have to pay.

“The legislative provisions of the A.C.A. are still in force until changed by the Congress,” the agency said in its reply to Mr. Huizenga. “Taxpayers remain required to follow the law and pay what they may owe.”