Like HHS, the State Department and the Environmental Protection Agency have maintained the freeze as a way of reducing their workforces and reshaping organizational structures after a directive last month from the Office of Management and Budget that said all federal agencies must submit a plan by June 30 to shrink their civilian workforces. HHS, State and EPA also face significant cuts in the Trump administration’s budget proposal for the fiscal year starting Oct. 1. The administration, which unveiled a “skinny budget” for fiscal 2018 in March, is scheduled to release its full budget next week.

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A senior CDC official said unfilled positions include dozens of budget analysts and public health policy analysts, scientists and advisers who provide key administrative support. Their duties include tracking federal contracts awarded to state and local health departments and ensuring that lab scientists have the equipment they need.

Though HHS has exempted many positions from the freeze, including physicians and personnel who respond to cybersecurity and public health emergencies, many support personnel who often play critical roles have been affected.

“It’s all the operational details,” said the official, who spoke on the condition of anonymity because CDC staff are not permitted to comment publicly without approval from HHS. The situation has been made worse, the official said, because the agency has been operating without a permanent director since Tom Frieden stepped down in January. That job is considered one of the most crucial public health positions in the government given the CDC's role in tracking and stopping infectious disease outbreaks in the United States and worldwide.

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When HHS Secretary Tom Price visited the Atlanta-based agency in April, the former Georgia lawmaker called CDC “an absolute jewel to our nation,” adding that its location in his home town “makes it extra special.” In a meeting with senior leaders, Price promised to name a director within the month.

But at least 125 job categories have been blocked from being filled, according to a recently released CDC document. Each covers multiple people. The document was released through a Freedom of Information Act request by the Sierra Club and reviewed by The Washington Post. Many of the unfilled jobs are high-level positions, at least GS-12 and above, according to the document.

Several positions are in the Office of Public Health Preparedness and Response, which regulates some of the world's most dangerous bacteria and viruses and manages the nation's stockpile of emergency medical countermeasures. Others include positions in the director's office, infectious disease offices and the office for noncommunicable diseases, injury and environmental health.

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The hiring freeze, imposed by an executive order that President Trump signed Jan. 22, covers currently open positions, prevents new positions from being created and blocks lateral transfers, officials said.

The Sierra Club's public health policy director, Liz Perera, said the administration’s “thoughtless freeze on hiring public servants prevented the CDC from filling critical roles at programs essential to preventing chronic and infectious diseases, advancing immunization and safeguarding environmental health.”

An HHS spokeswoman referred questions about the freeze to a May 2 speech by Price, who asked managers to review the efficiency of operations and draft plans to reduce staff. The budget process should be viewed as a way to “reimagine how we can do the work that we do and how we can do it better,” he told employees.

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“We’re not looking to achieve an arbitrary financial goal or workforce numbers,” Price said. “We’re certainly not gunning for specific programs or agencies.”

It’s unclear how many positions have been affected across HHS. At NIH, hiring is permitted for “essential patient care staff vacancies,” but reassignments are not allowed and contractors cannot be used for full-time duties, according to an internal NIH memo last month.

Some support positions, such as program assistants and laboratory assistants, remain vacant. Many of those personnel log in or handle patient specimens and issue reports, jobs that directly affect patient care, said a senior physician at the National Cancer Institute who spoke on the condition of anonymity for fear of funding retaliation.

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One such assistant who worked for the physician left late last year, but the institute has been unable to replace her because the human resources department “was overwhelmed by the demand and could not process recruiting actions,” the clinician said.

Recruitment for a senior laboratory position also has been held up “since it's complicated to get exceptions granted,” the doctor said.