The New York Times is declining a federal judge’s request that one of its reporters appear in court today to explain how he got front-page scoops about the internal communications of a pharmaceutical company.

The judge, Jack Weinstein of U.S. District Court in Brooklyn, had asked the reporter, Alex Berenson, to testify voluntarily about how he obtained the documents, which reportedly discuss health risks connected to the Eli Lilly drug Zyprexa. In the invitation to Mr. Berenson, Judge Weinstein suggests that the reporter engaged in “a conspiracy to obtain and publish” the Zyprexa documents.

Judge Weinstein, who is overseeing several lawsuits against Eli Lilly by users of the drug, had placed the documents under a protective order.

In a letter dated Monday, a Times attorney, George Freeman, told Judge Weinstein that Mr. Berenson would not be appearing in his courtroom today.

“As a matter of long-held principle, we believe that it would be inappropriate for any of our journalists voluntarily to testify about news gathering methods at the Times,” Mr. Freeman wrote.

Mr. Berenson received the Eli Lilly documents from an attorney in Alaska who had subpoenaed them from an expert witness for the plaintiffs in the Zyprexa lawsuits.

Judge Weinstein has not signaled how he will proceed, a lawyer involved in the case, Edward Hayes, said.

The judge’s responses could range from ordering Mr. Berenson to appear in court to dropping the issue and lifting his protective order.