“We obviously would have preferred to know, but the real issue here is the government’s intrusion into a reporter’s private communications,” Ms. Murphy said. “This should be a grave concern to anyone who cares about an informed citizenry.”

She added that Ms. Watkins would remain on her current beat, covering federal law enforcement.

“We support her,” Ms. Murphy said.

Ms. Watkins disclosed the relationship with Mr. Wolfe to The Times after she was hired, and before she started work at the paper on Dec. 18. On Thursday, Ms. Watkins told her editors that Mr. Wolfe was not a source of classified information for articles she had written during their relationship, which ended last year.

Ms. Watkins joined McClatchy Newspapers as an intern in 2013, and became a finalist for a Pulitzer Prize there two years later as part of a reporting team that revealed C.I.A. spying on the Senate Intelligence Committee.

She went on to cover national security matters, including the committee’s work, at The Huffington Post, BuzzFeed and Politico. The records seized by the Justice Department span her time at those news outlets, as well as her undergraduate years at Temple University, when she was a reporting intern in Washington.

Law enforcement officials did not obtain the content of the messages, according to the letter sent to Ms. Watkins by the Justice Department, but the information now in their possession — whom Ms. Watkins was communicating with, and when — could reveal her contacts. Reporters often rely on the trust of insiders who can offer insight into the workings of government, but often need their identities protected to preserve their livelihoods and, in some sensitive cases, avoid prosecution.

Under Mr. Obama, the Justice Department prosecuted more leak cases than all previous administrations combined. Mr. Trump’s attorney general, Jeff Sessions, said last year that the Justice Department was pursuing about three times as many leak investigations as were open at the end of the Obama era.