But, Mr. Baquet added, “We are troubled by Ali’s conduct, particularly while she was employed by other news organizations. For a reporter to have an intimate relationship with someone he or she covers is unacceptable.”

Ms. Watkins, who has not written for The Times since Mr. Wolfe’s arrest, was notified in February by the Justice Department that her email and phone records had been seized. On the advice of her personal lawyer, she did not inform her editors in The Times’s Washington bureau, and only revealed the information last month when her colleagues were about to report on Mr. Wolfe’s arrest. Mr. Baquet wrote that those actions “put our news organization in a difficult position.”

The government’s pursuit of Ms. Watkins — who at one point was confronted in a bar by a Customs and Border Protection officer, who seemed to have gained access to her private travel records — has outraged press advocates. But journalists were also unsettled by her violation of a bedrock norm of their profession: avoiding romantic involvement with a person she covered.

Reporters at The Times, and at other news organizations, have expressed unease over Ms. Watkins’s conduct. Women in particular say the episode has made them more vulnerable to an ugly and false stereotype often lobbed at female reporters, that they exchange sex for information.

Ms. Watkins met Mr. Wolfe while reporting on the intelligence committee as a 22-year-old intern at McClatchy Newspapers, where her coverage led to a series of stories named a finalist for a Pulitzer Prize.

She has said the relationship did not turn romantic until after those stories ran. During the relationship, she continued to cover the Senate Intelligence Committee for The Huffington Post, BuzzFeed News and Politico, telling editors at those organizations that she did not rely on Mr. Wolfe as a source. Last fall, after Ms. Watkins and Mr. Wolfe had broken up, she briefly dated another staff member at the intelligence committee, friends said.

Although her disclosures varied in detail, none of her editors barred her from covering the intelligence committee, or explicitly told her that the relationship was inappropriate.