Reporter Judith Miller, a central figure in the CIA leak investigation that resulted in the indictment of former vice presidential chief of staff I. Lewis "Scooter" Libby, is leaving the paper effective immediately, The New York Times confirmed to FOX News on Wednesday.

"We are grateful to Judy for her significant personal sacrifice to defend an important journalistic principle," said Arthur Sulzberger Jr., publisher of The New York Times. "I respect her decision to retire from the Times and wish her well."

"In her 28 years at the Times, Judy has participated in some great, prize-winning journalism," Bill Keller, executive editor of the paper, wrote in a memo released to staff. "She displayed fierce determination and personal courage both in pursuit of the news and in resisting assaults on the freedom of news organizations to report. She carries our best wishes into the next phase of her career."

The development comes after Miller was jailed for 85 days for refusing to testify before a grand jury investigating who leaked the name of CIA operative Valerie Plame Wilson. Miller was freed in September and ultimately answered questions before the panel, testifying that she did discuss Wilson and her husband, Amb. Joe Wilson, with Libby during three conversations in June and July of 2003.

While Miller initially enjoyed the paper's support, appearing before the U.S. District courthouse in Washington with Sulzberger, she quickly found herself on the losing end of a major dispute within the paper over how the matter was handled.

She was criticized harshly and publicly by other writers and editors at the Times who questioned her reporting on Iraq's weapons of mass destruction before the war and her actions in the CIA leak case. Several editors also said she was difficult to control.

In an Oct. 23 memo to staff, Keller wrote that Miller "seems to have misled" the newspaper's then Washington bureau chief, Phil Taubman, about whether she had received information about Plame Wilson's identity. Miller denied Keller's claims.

Sulzberger continued to defend Miller's decision to go to jail to protect Libby's identity and said the paper will continue to use confidential sources.

But in a speech last month, he added, "There's no question that the Times suffered" and its reputation was hurt by the cumulative effect of the ongoing controversy relating to Miller.

A letter from Miller is expected to be printed in the paper on Thursday. In it, she writes that she's leaving because she has "become the news, something a New York Times reporter never wants to be."

Miller joined the Times in 1977 and earned a Pulitzer Prize in 2001 for her work on the team that reported on the Sept. 11, 2001, terror attacks on America and profiled the threats from the global terrorism network.

FOX News' David Rhodes and The Associated Press contributed to this report.