Obamacare's tax audits are few and far between

Tax season is a pain in the neck for millions of people, but many Americans this year may be getting a pass from unpleasant questions—or even an audit—from the Internal Revenue Service about their compliance with Obamacare.

A leading tax audit defense company said its clients so far are seeing a surprisingly low rate of queries tied to the Affordable Care Act this year—the first in which Americans were asked to disclose their health insurance status.

TaxAudit.com also said the IRS has been asking the company's clients about just one of the several types of ACA-related issues that could trip filers up. Only people who received tax credits to buy Obamacare plans, but did not file one or two forms in conjunction with those subsidies are receiving IRS queries, the company said.

The agency thus appears to be forgoing, at least for now, recovering potential penalties or other payments from those TaxAudit.com customers for the other issues.

So far, none of the company's customers are being challenged about their claims to have had health insurance last year, about their exemption from Obamacare's mandate to have such insurance, or about the amount of money they received to help pay for their coverage.

"It's dialing for dollars," TaxAudit.com's vice president of customer advocacy, Dave Du Val, said of the grace period that most people seem be getting from the IRS about Obamacare compliance.

"You can't lose," said Du Val, whose company assists clients with questions and audits from the IRS. The company's services are available as part of Intuit's TurboTax tax preparation software.

Read MoreBig changes proposed for Medicare surgery payments

Du Val said he expects the agency has, to a certain extent, thrown up its hands, and is not aggressively enforcing compliance with Obamacare, at least for this year.

"I don't think they have the manpower now, I don't think they believe they have the manpower either," Du Val said.

Asked if he believed his client's customers were the only ones subject to an effective grace period this year from the IRS on most ACA-compliance issues, Du Val said, "No, not at all."

An IRS spokesman had no immediate comment when CNBC asked about TaxAudit.com's claims, but noted it takes time for the agency to process data from a filing season that includes about 150 million returns.

Last year was the first in which most Americans were required by the ACA to have some form of health coverage or be subject to a tax penalty equal to the higher of $95, or 1 percent of adjusted gross household income.

The collection of penalties and disclosure of insurance status only began earlier this year with the 2014 tax filing season. Most people were able to claim, truthfully, that they had insurance, and weren't required to file anything else.

But a fraction of people claimed an exemption for Obamacare's individual mandate, and were required to state the basis for that exemption, which can include having very low income, having filed for bankruptcy, being the victim of domestic violence or having a close family member die.

"The exemptions are so many, and so varied," Du Val said.

Taxes 1040 financial advisor
Comstock | Getty Images

This past season also was the first in which people who purchased insurance plans from Obamacare marketplaces, and who received a tax credit to help pay for their monthly premiums, were required to file new tax forms that reconcile what they received in subsidies with what they they should have actually received based on their incomes. Almost 90 percent of the more than 6 million Obamacare customers who were covered at the end of last year received such tax credits.

But just 5 percent of subsidized Obamacare customers were estimated to have received the correct amount of money from the federal government. The rest were expected to owe some of the subsidies back to the IRS, or to get even more money from the agency.

Du Val said that out of the 13,000 or so queries TaxAudit.com's clients have received so far from the IRS this year, only slightly more than 1 percent have been about ACA compliance.

"Truthfully, I'm a little surprised it's that low right now," Du Val said. He expected the IRS would be asking questions related to Obamacare of about 3 percent of the company's clients.

Customers are only being questioned by the IRS if they received tax credits to help pay for their Obamacare plan premiums, but failed, for whatever reason, to file a form reconciling the amount of money they received with what they should have gotten, or another form indicating that they or another person on their return did not have coverage for the entire year, he said.

Other people who received subsidies but who filed the required forms have not received queries from the IRS, Du Val said. That's been the case even if their returns relied on 1095-A forms—which detailed how much they got in subsidies over the course of the year—that contained incorrect information.

"We've seen lots of people, the 1095-A is not right, we know it's not right," he said.

Read MoreObamacare lowers uninsured rate, yet again

Earlier this year, the Obama administration revealed that hundreds of thousands of 1095-A forms it had sent out to Obamacare plan customers contained errors about the subsidies that people received. The administration said it would not penalize people for having already filed income tax returns based on incorrect 1095-A forms, but also urged people to check to see if they might be eligible for a bigger tax credit it they had done so.

Also not being questioned are people who may have lacked insurance for part of the year, but stated they were insured during the full year, or people who may not be eligible for the exemptions from the coverage mandate that they claimed, Du Val said.

While he is surprised about the low rate of ACA-related questions by the IRS, he is less surprised by the agency's apparent lack of aggression in challenging people, or at least TaxAudit.com customers, on their compliance with the mandate or on the amount of tax credits they received this year.

"It's a big project," Du Val said of the ACA. "There's always going to be errors in something like that."

"My best guess is the IRS isn't set up for it yet."

Given the inaccuracies in many of the 1095-A forms the government sent filers, and other complicated questions related to Obamacare, the IRS has to look at what level of questioning taxpayers is "worth doing," he said.

But in future years, Du Val said, "Those audits are coming."

Read MoreHigher costs for Obamacare's new Medicaid patients

He noted that the IRS will have help making sure people are complying with the ACA's rules this year because insurance companies and employers will be filing forms with the government indicating who is covered by their plans.

"I truly think they're not going to get a grace period this coming year," Du Val said of tax filers and their compliance with the ACA.