WASHINGTON — The Obama administration is struggling to resolve widespread data discrepancies that could call into question coverage for millions under the health overhaul, the government’s health care fraud watchdog reported Tuesday.

In a pair of reports, the Health and Human Services inspector general found that key personal details submitted by many consumers do not match up with records the government has on file.

It also found shortcomings in the internal safeguards used by the federal insurance exchange and some state marketplaces to check the accuracy of information submitted by consumers. That’s critically important, because it can affect an individual’s eligibility for taxpayer-subsidized health insurance.

The reports marked the first independent look at a festering behind-the-scenes issue that could turn into another health law headache for the White House.

The problem is one of the top challenges facing newly installed HHS Secretary Sylvia Mathews Burwell. The administration says it is making daily progress to clear the issues, and that may not be completely reflected in the reports.

The inspector general said the federal insurance exchange reported a total of 2.9 million so-called “inconsistencies” with consumer data from October through December 2013.

Officials had the technical capability to resolve roughly 330,000 of those cases, but only about 10,000 cases were actually closed during the period covered by the report.

Several states running their own insurance markets also were having problems clearing up data discrepancies.

Most of the issues dealt with citizenship and income information supplied by consumers that conflicted with what the federal government has on record, the report said.

President Barack Obama celebrated 8 million sign-ups as proof that technical problems which initially kept many consumers from enrolling had finally been overcome. It now turns out that some of those problems continued, only out of sight. The inspector general said the efforts of the administration and states to clear up the discrepancies were complicated by lingering computer issues.

“The federal marketplace was generally incapable of resolving most inconsistencies,” the report said.

The inspector general’s inquiry was requested by congressional Republicans as a condition of ending the budget standoff that partially shut down the government last fall. Republicans say they are concerned that people who are not legally entitled to the law’s government-subsidized private health insurance could nonetheless be getting it.

“This report is one more example of just how flawed the president’s health care law is,” Senate Republican Leader Mitch McConnell said in a statement. “Whatever one’s opinion of Obamacare, the American public deserves to know that their tax dollars are allocated appropriately and that public officials take their responsibility to accurately and faithfully apply the laws enacted by Congress seriously.”

The inspector general stopped short of drawing sweeping conclusions.

“Inconsistencies do not necessarily indicate that an applicant provided inaccurate information … or is receiving financial assistance through insurance affordability programs inappropriately,” the report said.

However, the watchdog office called on the administration to publicly explain how and by what date it will resolve the data problems in the 36 states where Washington is operating new insurance markets.

In a written response to the report, Medicare chief Marilyn Tavenner said the administration concurs with the recommendations and is working on a plan. Tavenner also said that some of the computer issues that were getting in the way of resolving the problems have now been overcome.

“It is not surprising that there are inconsistencies between some information provided by application filers and the (government’s) electronic data sources,” she said. Officials say most discrepancies are cleared up in favor of the consumer.

The law provides the administration with the option of extending an initial 90-day period for resolving data issues.

The inspector general also found that:

—Early on, the government’s eligibility system was “not fully operational.” As a consequence, even if a consumer supplied the appropriate documentation, officials were not able to close the case.

—States running their own insurance markets had a mixed record of dealing with eligibility problems. Of the 15, including Washington, D.C., seven said they cleared up problems without delay. Four said they were unable to resolve inconsistencies. Some did not supply any information.

—Most of the data discrepancies in the federal market had to do with citizenship and immigration status. Only citizens and legal immigrants can receive coverage under the law. More than 40 percent of the problems involved citizenship and immigration information. Income was the next category, accounting for one-third of the problems.

—The federal insurance exchange didn’t always verify Social Security numbers through the Social Security Administration, as required by its own internal safeguards. The California marketplace didn’t always verify citizenship and legal presence through Homeland Security.