Nearly 700 positions are vacant at the Centers for Disease Control and Prevention because of a continuing freeze on hiring that officials and researchers say affects programs supporting local and state public health emergency readiness, infectious disease control and chronic disease prevention.

The same restriction remains in place throughout the Health and Human Services Department despite the lifting of a government-wide hiring freeze last month. At the National Institutes of Health, staff say clinical work, patient care and recruitment are suffering.

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.

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.