Mr. Holder’s Justice Department pursued at least nine leak-related prosecutions, more than all previous administrations combined. The current attorney general, Jeff Sessions, said in August that the Justice Department would vastly expand that effort. He also promised to revisit rules that restrict investigators’ ability to obtain reporters’ records, saying the role of the press “is not unlimited.”

Until last week, though, Mr. Sessions’s rhetoric had seemed just that.

Prosecutors seized Ms. Watkins’s records as part of an investigation into whether a former Senate Intelligence Committee aide, James A. Wolfe, had given classified materials to reporters. Mr. Wolfe was arrested on Thursday on charges of lying to investigators; he has denied leaking classified materials. Ms. Watkins and Mr. Wolfe were in a three-year relationship that ended last year, before she was hired by The Times.

The seizure of the reporter’s communications — data that stretched back to her undergraduate days, when she reported on the Senate Intelligence Committee as an intern — struck press rights groups as ominous. The advocates said that the government’s actions seemed severe, given that the Justice Department has not yet charged anyone with leaking classified information in this case.

Ms. Watkins received a letter from the Justice Department in February informing her that it had seized records from two email accounts and a phone number of hers. Ms. Watkins, after consulting with her personal lawyer, did not tell her editors about the letter until late last week. It was sent about two months after F.B.I. agents approached her about Mr. Wolfe; she said she did not answer their questions at the time.

Sarah Isgur Flores, a Justice Department spokeswoman, said on Sunday that the department had “fully complied” with its internal guidelines in deciding to seize Ms. Watkins’s records. Three other reporters were also cited in Mr. Wolfe’s indictment; the Justice Department said their records were not subject to subpoenas.

The guidelines installed by Mr. Holder state that reporters must be informed ahead of time before the government obtains their records, giving them a chance to negotiate the scope of the request or to challenge it in court.