The C.D.C. will undergo a comprehensive re-evaluation, the agency’s director said.

But the agency’s infrastructure was neglected for decades, like the nation’s public health system generally, and the pandemic has posed unprecedented challenges. Early on, the C.D.C. made key mistakes in testing and surveillance — for example, famously fumbling design of a diagnostic kit sent to state laboratories.

Officials were late to recommend masking, partly because agency scientists didn’t recognize quickly that the virus was airborne. In May of last year, Dr. Walensky announced that vaccinated people could take masks off indoors and outdoors; just weeks later, it became clear that vaccinated people could not only get breakthrough infections but also could transmit the virus.

In August, Dr. Walensky joined President Biden in supporting booster shots for all Americans, before scientists at the Food and Drug Administration or her own agency had reviewed the data on whether they were needed.

More recently, the highly contagious Omicron variant has led the C.D.C. to issue recommendations based on what once would have been considered insufficient evidence, amid growing public concern about how these guidelines affect the economy and education.

In December, the C.D.C. shortened the isolation period for infected Americans to five days, although it appears that many infected people can transmit the virus for longer. Over the past few weeks, some experts have criticized the agency for changing the metrics used to assess risk and determine appropriate local measures, in order to appease business and political interests.