By Louise Radnofsky 

WASHINGTON--Marilyn Tavenner, head of the U.S. agency that oversees the federal health law along with Medicare and Medicaid, said Friday she would step down in February, leaving a temporary administrator in the post until the White House and Senate Republicans can agree on a successor.

Ms. Tavenner became the first permanent head of the Centers for Medicare and Medicaid Services in more than six years when she was confirmed in 2013--after working more than a year in an acting capacity. She continued to enjoy Republican support through the rollout of the health law's insurance exchanges.

Andy Slavitt, a former top executive at UnitedHealth Group who is now the second-highest-ranking official in the agency, will take over as acting administrator, agency officials said.

Both the Obama administration and the George W. Bush administration have faced problems getting CMS heads confirmed. A fresh confirmation process could be turbulent because many Republicans in the GOP-controlled Senate are pressing for major changes to the 2010 health law.

In a warning shot to the White House, Senate Majority Leader Mitch McConnell (R., Ky.) said in a statement that "we now call on the president to nominate someone whose sole focus will be to look out for our nation's seniors and the many vulnerable Americans who use these programs, and not distract them from that task with Obamacare."

White House spokeswoman Jessica Santillo said President Barack Obama wouldn't immediately announce a nominee to succeed Ms. Tavenner. "We are confident, when we have a nominee, he or she will be worthy of quick consideration and bipartisan support," she said.

Mr. Slavitt, 48 years old, was group executive vice president at Optum, a unit of insurer UnitedHealth and the parent company of Quality Software Services Inc., when the contractor was picked to lead the cleanup effort when HealthCare.gov was crippled by technology troubles. He was brought in-house in 2014 as one of the first hires of new Health and Human Services Secretary Sylvia Mathews Burwell, and quickly took on preparations for the second main open-enrollment period for the health law, which started relatively smoothly in mid-November.

Ms. Tavenner had been Virginia's health secretary before joining CMS in 2010. She started her career as a nurse and rose to executive positions in the for-profit hospital sector.

At the time of her nomination, she was considered among the least-controversial candidates to succeed Don Berwick, who never got Senate confirmation and remained acting administrator for more than a year. News of Ms. Tavenner's decision to leave was first reported by the Huffington Post.

Ms. Tavenner, 63, didn't give a reason for her departure in a farewell email to CMS staff. She listed a series of agency accomplishments under her tenure, including slowing the growth of health-care costs, now at a historically low rate. She also praised the current operation of the health law's online insurance exchanges. But problems with the law's rollout have continued to dog her, including her overestimating the number of people who had coverage through the exchanges in congressional testimony last fall.

She wasn't immediately available for an interview on Friday.

Ms. Tavenner recently has faced scrutiny over Medicare operations. A Wall Street Journal article last month highlighted her intervention in Medicare fraud investigations after being contacted by elected officials.

In one case, Ms. Tavenner instructed deputies to restore blocked Medicare payments to Houston's Riverside General Hospital in 2012, even as the agency was cooperating in a criminal investigation of the facility, according to former investigators and documents obtained by the Journal. The hospital's top executive was indicted in a $158 million fraud scheme two months following the order, and the chief executive was convicted in October.

In a statement at the time, Ms. Tavenner said the Riverside episode "reflected the tension between fraud prevention and access to care." She also said that she was unaware of the pending indictments.

Tom Scully, who served as the CMS administrator for three years during the George W. Bush administration, said Ms. Tavenner had been thinking about leaving for around six months. "Five years is a long time, and I can't imagine anyone doing that job for five years," he said.

Christopher S. Stewart contributed to this article.

Write to Louise Radnofsky at louise.radnofsky@wsj.com

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