(Bloomberg) — Sylvia Mathews Burwell was confirmed Thursday by the U.S. Senate as the secretary of the Department of Health and Human Services, replacing Kathleen Sebelius and signaling a new stage for Obamacare.

The vote for Burwell, currently President Barack Obama’s budget chief, was 78-17. Most Republicans supported her while making clear their votes didn’t reflect backing for the Affordable Care Act, known as Obamacare.

Burwell, 48, assumes control of a government agency with close to a $1 trillion annual budget and programs touching the lives of every American. Her priority is the Affordable Care Act, which enters its second year of enrollment under continuing political attack and with a technology infrastructure that remains a work in progress.

“Ms. Burwell has a reputation for competence, and she is going to need it,” Sen. Lamar Alexander, a Tennessee Republican, said in a floor speech Wednesday. “She is being asked to oversee a big mess this administration has created in health care and so far has lacked the leadership to clean up.”

About 8 million people signed up for private health coverage under the ACA this year, after the administration fixed errors with its consumer website, Healthcare.gov, that stymied enrollment in October and November. Behind the scenes backend technology is still under construction to allow the site to communicate with insurers and correct mistakes in applications. Some states, meanwhile, are struggling with a backlog of applications for Medicaid, the program for low-income people, after it was expanded this year.

Application issues

Yesterday, the U.S. Centers for Medicare and Medicaid Services, an agency under Burwell’s purview that runs Obamacare, said more than 2 million people, a quarter of the enrollment total, have “inconsistencies” in the information they provided about their income, citizenship or immigration status.

The agency is allowing an indefinite amount of time for those people to provide documents supporting their applications.

Sebelius long ago exhausted any goodwill she enjoyed from Republicans, who used debate on Burwell’s nomination to assail the Obama administration’s implementation of the health law.

“They have yet to put in place a mechanism to ensure that the people who are getting subsidies under Obamacare are eligible for them,” Sen. Rob Portman, an Ohio Republican, said Wednesay in a floor speech. “Secretary Sebelius made certain commitments there. These verification methods are not in place.”

Republican requests for information about the implementation had been met by “silence, stonewalling, no transparency,” the senator said.

Republican support

Like other Republicans, Portman had no venom for Burwell, whom he said he would support. She “is a manager and I think she’s what we need at the Department of Health and Human Services,” he said.

Democrats offered a defense of the law, asserting that Republicans were ignoring or misleading the public about its benefits. Sen. Ben Cardin, a Maryland Democrat, said the law had expanded insurance coverage, was in part responsible for reducing the growth of national health care spending since 2009, and had helped cut the federal budget deficit.

“My friends on the other side of the aisle, their answer unfortunately is ‘repeal, repeal, repeal,’” he said in a floor speech. “They have no plan for health care in this country.”

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