An interim U.S. attorney is demanding information about the selection of research articles and the role of N.I.H. Experts worry this will have a chilling effect on publications.

A federal prosecutor has sent letters to at least three medical journals accusing them of political bias and asking a series of probing questions suggesting that the journals mislead readers, suppress opposing viewpoints and are inappropriately swayed by their funders.

The letters were signed by Edward Martin Jr., a Republican activist serving as interim U.S. attorney in Washington, D.C. He has been criticized for using his office to target opponents of President Trump.

Some scientists and doctors said they viewed the letters as a threat from the Trump administration that could have a chilling effect on what journals publish. The health secretary, Robert F. Kennedy Jr., has said he wants to prosecute medical journals, accusing them of lying to the public and colluding with pharmaceutical companies.

One of the letters was sent to the journal Chest, published by the American College of Chest Physicians. The New York Times obtained a copy of the letter.

The Times confirmed that at least two other publishers had received nearly identically worded letters, but those publishers would not speak publicly because they feared retribution from the Trump administration.

In the letter to Chest, dated Monday, Mr. Martin wrote, “It has been brought to my attention that more and more journals and publications like CHEST Journal are conceding that they are partisans in various scientific debates.”