And even as she divested from many holdings in health-related companies, some members of Congress continued to express concern that those investments could compromise her positions on a variety of agency matters.

“It is unacceptable that the person responsible for leading our nation’s public health efforts has, for months, been unable to fully engage in the critical work she was appointed to do,” Senator Murray said Wednesday. “Dr. Fitzgerald’s tenure was unfortunately the latest example of the Trump administration’s dysfunction and lax ethical standards.”

But Dr. Fitzgerald’s predecessor at the C.D.C., Dr. Tom Frieden, issued a statement that suggested the latest investments causing concern were made by a portfolio manager without Dr. Fitzgerald’s knowledge. In August, financial disclosures show she purchased stocks in several companies that might conflict with her activities at the agency, including Japan Tobacco, the drugmaker Merck, and Humana, the health insurer. The records show she then sold those and other health stocks in October.

“I have spoken with Dr. Fitzgerald and believe her when she says that she was unaware that a tobacco company investment had been made,” Dr. Frieden said. “She understands that any affiliation between the tobacco industry and public health is unacceptable, and that when she learned of it, she directed that it be sold.”

But Craig Holman, the government affairs lobbyist for Public Citizen, the consumer advocacy group, said not knowing about the investments a manager is making on your behalf is not an excuse. “You cannot just say the manager can do whatever he or she wants to do as long as I don’t know about it,” he said. “That’s not the conflict of interest code.”

The tobacco-related investments alarmed others. “It’s astonishing that the director of the Centers for Disease Control, which plays a major role in reducing tobacco use, would purchase stock in a tobacco company,” said William B. Schultz, a former general counsel for H.H.S.

The agency has been tackling several tough issues this year, including potential budget cutbacks and a flu epidemic that claimed more lives this week and closed some schools across the country. About 80 percent of the cases this season are of the H3N2 strain, and officials said last week the rate of hospitalization among flu sufferers was particularly high this year. The agency plays a critical role in tracking the number of illnesses and deaths and helping coordinate the public health response.