All of the health plans offered by Obamacare exchanges in five states include coverage for abortions in a potential violation of the law that says at least two plans must be available to consumers who don’t want any association with the controversial procedure, according to a government audit released late Monday.

Altogether, more than 1,000 Obamacare plans offer abortion coverage in 28 states that don’t prohibit it, the Government Accountability Office said, including 95 percent of the plans in California and all of the plans in Vermont, Connecticut, Rhode Island, Hawaii and New Jersey.

Under the Affordable Care Act, the government is supposed to ensure at least two multistate plans that don’t include abortion coverage are available in those states. There is a four-year transitional period for the administration to implement multistate plans, so it is not yet a violation of the law at this juncture, according to a congressional aide.

Rep. Christopher H. Smith, a New Jersey Republican who opposes taxpayer funding for abortions, said the sheer number of exchange plans that cover abortion, with taxpayer-subsidized premiums, shows government money is going to pay for the procedure despite President Obama’s insistence that wouldn’t happen.

“No one likes to be misled or deceived,” he said.

The Health and Human Services Department, in its official response to the GAO’s report, acknowledged that “additional clarification may be needed” to make sure states and insurers are complying with the law.

The department’s Centers for Medicare and Medicaid Services, known as CMS, “will speak directly with the [qualified health plans] or state departments of insurance regarding the issues identified by GAO to determine whether additional guidance is necessary to ensure that states and issuers understand the laws and regulations governing the coverage of nonexcepted abortion services,” Jim R. Esquea, assistant secretary for legislation at HHS, wrote to the GAO.

Efforts to reach some of the states named in the report were unsuccessful late Monday. A separate survey by the conservative Family Research Council found that, in the case of Hawaii’s state Obamacare exchange, all 39 of the insurance plans this year include coverage of elective abortions.

Abortion coverage was a thorny issue when Democrats were writing the Affordable Care Act in 2009 and 2010, and it almost blocked passage of the bill in the House when pro-life Democrats balked at the prospect of taxpayer subsidies for abortions in the national health law.

Mr. Obama finally promised an executive order vowing to follow the so-called Hyde language, which prohibits federal funding for abortion.

Mr. Smith said that while the Treasury isn’t cutting a check to directly pay for abortions, the second part of the Hyde Amendment says no funds “shall be expended for health benefits coverage that includes coverage of abortion.”

The GAO report found that 1,036 qualified Obamacare health plans in 28 states covered “nonexcepted” abortions, meaning all cases except where the pregnancy is the result of rape and incest, or because the life of the woman is in danger.

The report said 1,062 health plans did not cover the procedure in those states.

Qualified health plans can cover nonexcepted abortions, the GAO said, but there are conditions. For instance, to pay for the services, issuers must collect no less than $1 per enrollee per month.

The auditors found various inconsistencies on that front. Two issuers told the GAO they did not round up their estimated costs for abortions to at least $1 and were not using the statutory minimum for determining how much to collect from enrollees.

Another issuer estimated the costs for abortion services to be $1.10 per enrollee and charged between 51 cents and $1.46, depending on the health plan.

In one instance, the Washington Health Benefit Exchange’s billing system was not assessing an extra premium to those whose health premiums were fully subsidized under Obamacare and whose plans covered nonexcepted abortion services. The Washington state exchange told auditors they will work with the IRS to reconcile any amounts owed by applicable taxpayers in 2014 and 2015 and change their billing practices in time for 2016.

The GAO found that information on abortion services varied. Some asked consumers to directly contact an issuer to find that information instead of offering it upfront, and a few issuers told GAO they had not been aware of a provision that requires them to notify enrollees that abortions were a covered benefit.

“There is no transparency, if you read this report,” said Rep. Joseph R. Pitts, Pennsylvania Republican.

Mr. Obama lost a key court case earlier this year when the Supreme Court ruled the administration could not insist that closely held corporations cover contraceptive services for their employees if they held a valid religious objection to paying for it. While some businesses objected to all contraceptives, others protested only a subset that included the morning-after contraceptive pill, which they argue can sometimes induce abortion.

The justices, in a 5-4 ruling, held that the Religious Freedom Restoration Act required the government to do more to accommodate those employers’ concerns.

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