The move came three weeks after the paper's Web site carried a lengthy story by Pulitzer Prize-winner Chuck Philips, who wrote that associates of Combs had arranged the assault on Shakur because they were angry that he had rejected overtures to sign with Combs' Bad Boy Records label.
Combs immediately called the Times story "beyond ridiculous and ... completely false." He strongly denied any involvement in the attack.
The paper quickly launched an investigation, and Philips issued an apology on March 27, as did his supervisor, deputy managing editor Marc Duvoisin.
Monday's retraction, in which the Times reiterated its apology, involves the March 17 story, which has been removed from its Web site, as well as a shorter version that appeared in print two days later. It also retracted comments made by Philips in two online chats as well as a blog.
A Times spokeswoman said Philips would continue to write for the newspaper. Asked about disciplinary action against him or others, she issued a statement from editor Russ Stanton saying the Times took the matter "very seriously," and the retraction and apology "speak for themselves."
The Smoking Gun story -- posted at http://www.thesmokinggun.com -- said the FBI documents were created by one of the subjects in the Times' report, James Sabatino, who is now in jail for wire fraud and racketeering.
The documents had black marks covering the name of the agent or agents who prepared them, appeared to be created in part with a typewriter, and were "nowhere to be found" in the FBI's computer system, according to The Smoking Gun.
Shakur, a charismatic singer and actor, survived a beating and gunshot wounds to the groin, head, hand and thigh during the 1994 attack. He was killed two years later in an unsolved drive-by shooting in Las Vegas.
The hoax marks a baptism by fire for Stanton, an insider who took over as editor of the fourth-largest paper in the United States in February, a month after the departure of the third editor in less than three years. Newsroom morale has plunged as the paper's owners seek to cut costs.
The paper's Tribune Co. parent was taken private last December in a deal led by Chicago billionaire Sam Zell. The deal left Tribune saddled with $13 billion of debt at a time when the economy appears headed into a recession.
Reuters/Nielsen
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