In a meeting with senior staff, Dr. Walensky outlined in broad terms a plan to reorganize the agency’s structure to prioritize public health needs and efforts to curb continuing outbreaks, and to put less emphasis on publication of scientific papers about rare diseases.

The steps announced on Wednesday grew out of an external review Dr. Walensky had ordered in April, after months of scathing criticism of the C.D.C.’s response to the pandemic. Its public messages on masking and other mitigation measures were sometimes so confusing or abruptly modified that they seemed more like internal drafts than carefully considered proclamations.

The public guidance has been “confusing and overwhelming,” according to a briefing document provided by the agency.

Leaders of the agency’s Covid team rotated out after only a few months, leaving other senior federal health officials unsure about who was in charge. And important data were sometimes inexplicably released too late to inform federal decisions, including some data on breakthrough infections that could have influenced a recommendation on whether to authorize a round of booster shots.