A special prosecutor investigating the leak of a CIA operative’s identity concluded earlier this year that the Vice President’s chief of staff, I. Lewis Libby, deliberately failed to intervene with a New York Times reporter jailed for refusing to testify in the probe because it would not be to his advantage for her to speak freely, according to a letter obtained by The New York Sun.

However, the prosecutor, Patrick Fitzgerald, said in the previously undisclosed letter that he later came to suspect that the standoff might be due to a misunderstanding between attorneys for Mr. Libby and the reporter, Judith Miller.

Ms. Miller, who spent nearly three months in jail, was released last week after she agreed to testify to a grand jury investigating whether White House officials disclosed the identity of a CIA operative, Valerie Plame. Ms. Miller said she testified only after speaking directly with Mr. Libby and being convinced that he wanted her to do so.

The turn of events appears to have been triggered, at least in part, by Mr. Fitzgerald’s September 12 letter to Mr. Libby’s attorney, Joseph Tate of Philadelphia. In the letter, the prosecutor noted that while Mr. Libby personally released another reporter, Matthew Cooper of Time Magazine, from any obligation of confidentiality at Mr. Cooper’s request, Mr. Libby did not appear to have done so for Ms. Miller, even as she passed her days behind bars.

“I had assumed that Mr. Libby had simply decided that encouraging Ms. Miller to testify was not in his best interest,” Mr. Fitzgerald wrote. He also noted press accounts that suggested that Ms. Miller and her attorneys were not satisfied with the generic written waiver that Mr. Libby had signed. The prosecutor said his conclusion was also supported by the fact that Mr. Libby had apparently not reached out to Ms. Miller, despite the fact that several congressmen called on the White House aide to make such an effort.

Mr. Fitzgerald said that was his view for most of the summer, but he later became concerned that “there might be a failure of communication regarding the waiver.” He went on to cite a Los Angeles Times story that a lawyer for another White House source caught up in the probe, Karl Rove, was reluctant to contact Mr. Cooper out of fear that such a move might be viewed as an attempt to obstruct the investigation.

“It may be,” the prosecutor surmised, “that Ms. Miller remains in jail because of a misunderstanding.”

“I wish to make certain that you understand that if Mr. Libby maintains his waiver is valid and he wishes to communicate that fact either through you or directly to Ms. Miller or her counsel (without discussing the substance of what her testimony might be), I would not view such a communication as obstruction,” Mr. Fitzgerald wrote. The prosecutor said he couldn’t force Mr. Libby to contact Ms. Miller, but said if he did not, it implied “he would prefer that the status quo continue and Ms. Miller remain in jail rather than testify about their conversations.”

A spokesman for Mr. Fitzgerald, Randall Samborn, declined to comment on the letter yesterday.

Mr. Libby’s attorney, Mr. Tate did not return a message seeking an interview. However, in a written reply to Mr. Fitzgerald, Mr. Tate said he was baffled by the prosecutor’s missive. “To say I am surprised at its content is an understatement,” Mr. Tate wrote in his September 16 letter, made public by the Times last week. He insisted that he unequivocally reaffirmed the waiver to a lawyer for Ms. Miller more than a year earlier. “Neither my client nor I imagined that her decision to go to jail could be affected by anything that we could do,” Mr. Tate said.

While Mr. Fitzgerald admonished Mr. Libby not to discuss with Mr. Miller the substance of her testimony, a letter Mr. Libby sent to Ms. Miller on September 15 did mention what other reporters have said about their contact with the White House aide. “The public report of every other reporter’s testimony makes clear they did not discuss Ms. Plame’s name or identity with me or knew about her before our call,” Mr. Libby wrote. “I believed a year ago, as now, that testimony by all will benefit all.”

An attorney for Ms. Miller, Floyd Abrams, said in an interview yesterday that Mr. Fitzgerald’s letter set in motion the talks that led to the reporter’s release. “After this letter, negotiations really began in seriousness,” Mr. Abrams said. The discussions led to a phone conversation between Ms. Miller and Mr. Libby, with attorneys for both parties on the line.

Mr. Abrams said another important factor in Ms. Miller’s agreement to testify was Mr. Fitzgerald’s willingness to respect the confidentiality of the reporter’s other sources. “He agreed to focus his questioning on Libby,” Mr. Abrams said. “The real protection we were getting was other sources with whom she spoke at about the same time, though not on this particular matter.”

Mr. Fitzgerald’s letter said Mr. Libby has acknowledged speaking with Ms. Miller on July 8,2003, at the St. Regis Hotel, presumably in Washington, and by telephone on July 12, 2003. Ms. Plame was first identified publicly as a CIA employee by a syndicated columnist, Robert Novak, on July 14, 2003. Ms. Miller never published a story about the matter.