Robert F. Kennedy Jr., who recently took over as HHS secretary, said in an announcement about the changes that HHS will do more at a lower cost.

"We aren't just reducing bureaucratic sprawl," Kennedy said. "We are realigning the organization with its core mission and our new priorities in reversing the chronic disease epidemic."

HHS announced plans to cut only about 300, or 4.6%, of the 6,529 positions at CMS.

The CMS job cuts will have "a focus on reducing minor duplication across the agency," HHS officials said in a fact sheet. "This reorganization will not impact Medicare and Medicaid services."

Officials did not talk about how the cuts might affect the Center for Consumer Information and Insurance Oversight, the agency in charge of running Affordable Care Act programs, or HealthCare.gov, the federal agency that provides ACA public exchange services for residents of states that have not set up locally run ACA exchange programs.

HHS is planning for much deeper staffing cuts and realignments at agencies such as the Office of the Assistant Secretary for Health, the Health Resources and Services Administration, the Substance Abuse and Mental Health Services Administration, the Agency for Toxic Substances and Disease Registry and the National Institute for Occupational Safety and Health. HHS is putting NIOSH and the other agencies in a new Administration for a Healthy America.

The U.S. Centers for Disease Control and Prevention, an agency that now has about 12,600 employees, could lose about 2,400, or 19%, of its positions.

The CDC will have a "focus on returning to its core mission of preparing for and responding to epidemics and outbreaks," officials said. Officials noted that, in addition to facing position cuts, CDC will be gaining about 1,000 employees coming over from the Administration for Strategic Preparedness and Response.

Officials did not see how the CDC position cuts would affect the CDC's National Center for Health Statistics and or the center's National Vital Statistics System. Health insurers, benefit plan administrators and health plan actuaries depend heavily on CDC health data programs to analyze health risks and allocate resources.

The Senate Finance Committee recently endorsed the nomination of Dr. Mehmet Oz to be the next CMS administrator by a 14-13 vote. Only the Republicans on the committee voted for the nomination. At press time, Senate leaders had not yet said when they would bring the nomination to the Senate floor.

Related: Dr. Oz addresses concerns, discusses prior authorizations, at CMS confirmation hearing

Oz is a cardiothoracic surgeon who went on to become known to the general public as a television talk show host.

More cuts or other staffing changes at CMS could be announced once Oz is confirmed as the CMS administrator.

No additional cuts at HHS agencies are currently planned, "but the department will continue to look for further ways to streamline its operations and agencies," HHS officials said.