The paper has published a letter from Ms Miller explaining her position, as part of the agreement.
The Pulitzer Prize-winning journalist went to jail for 85 days rather than name her source in the CIA leak case.
Her source on the CIA leak story was I Lewis “Scooter” Libby, the former chief of staff to Vice President Dick Cheney.
He was charged on October 28 with obstructing justice, perjury and lying.
The national security writer for The Times, she was criticised for stories she wrote on weapons of mass destruction in Iraq that echoed Bush administration stances and turned out to be based on faulty intelligence.
Ahmad Chalabi, the Iraqi leader accused of giving US officials flawed information about Saddam Hussein’s weapons program, was a source on pre-war Iraq for Ms Miller.
In her letter, she said she had become a “lightning rod for public fury over the intelligence failures that helped lead our country to war” and wanted to leave the paper because she had “become the news”.
One of the newspaper’s editors was quoted in The Times as saying the paper had been hurt by delays in “coming clean” over lapses in its reporting.
The New York Magazine wrote in June 2004 that Ms Miller produced “stunning stories about Saddam Hussein’s ambition and capacity to produce weapons of mass destruction, based largely on information provided by Chalabi and his allies – almost all of which have turned out to be stunningly inaccurate.”
The conjecture over her reporting is another blow to the paper’s reputation.
The New York Times, which prides itself on being America’s paper of record, is still trying to restore credibility lost after former reporter Jayson Blair was found to have fabricated and plagiarised
dozens of news stories.