Some people also said that some effort to tone down language might make sense when appealing for funding from Republican conservatives in Congress.

The C.D.C. budget documents are circulated to other agencies and Congress and submitted to the Office of Management and Budget in the Trump administration. The budget office did not respond to a request for comment.

There seemed to be confusion around the public health agencies about whether the ban originated at the agency’s parent department, Health and Human Services, or inside the C.D.C. itself; and whether such a ban would apply beyond budget documents. The Food and Drug Administration was quick to note that it had gotten no such instruction. An agency spokeswoman, Jennifer Rodriguez, said, “We haven’t received, nor implemented, any directives with respect to the language used at F.D.A. to describe our policy or budget issues.” The National Institutes of Health referred inquiries to Health and Human Services.

Since the Trump administration has taken office, officials at the country’s premier disease-fighting agency have privately complained that it has come under various pressures, most involving Mr. Trump’s “America First” stance and his dislike of foreign aid rather than basic science itself.

Although Mr. Trump’s first “skinny budget” proposed deep cuts in medical work done overseas, it is not clear that he is going to get his way. Many legislators have recognized the value of detecting and fighting outbreaks abroad before they reach American shores, and the President’s Emergency Plan for AIDS Relief, which was created by President George W. Bush, is a favorite with Christian conservatives in Congress. Many of the hospitals helped in Africa were founded by Christian missionaries. As a former Indiana representative, Vice President Pence was among the agency’s strongest backers.

Even during the Obama administration, C.D.C. officials were required to clear most statements through Health and Human Services.

Under Thomas E. Price, Mr. Trump’s first secretary of Health and Human Services, the department seemed preoccupied with killing the Affordable Care Act. Mr. Price resigned in September after he was criticized for his expensive air travel. During his early tenure, the C.D.C. was run by an acting director, Dr. Anne Shuchat, who had been deputy to the former director, Dr. Thomas R. Frieden.