Seattle Weekly editor-in-chief Mark D. Fefer announced in Wednesday's issue that Molly Norris' comic would no longer appear in the paper.
Fefer wrote that the FBI advised Norris to move, change her name and wipe away her identity because of a religious edict issued this summer that threatened her life.
"She is, in effect, being put in a witness-protection program - except, as she notes, without the government picking up the tab," Fefer wrote. He told The Associated Press on Thursday that he had nothing further to say because it's a sensitive situation.
The FBI also declined to comment Thursday. David Gomez, the FBI's special agent in charge of counterterrorism in Seattle, told the New York Daily News in July that the agency was doing everything it could to protect individuals on a fatwa list issued by Yemeni-American cleric Anwar al-Awlaki.
Awlaki said in the June issue of English-language Muslim youth magazine "Inspire" that Norris is a "prime target" who should reside in "Hellfire."
Norris' cartoon inspired a Facebook page that caught the attention of authorities in Pakistan, who banned the social networking site in response.
Most Muslims regard any depiction of the prophet, even favorable ones, as blasphemous.
The Facebook page encouraged people to post images of Mohammed to protest threats against the creators of the American TV series "South Park" for depicting the prophet in a bear suit during an episode earlier this year.
Although the Facebook page was taken down by its creator, references to the page and to Norris' cartoon remain online.
Norris wrote in a post on her website that she meant her work only to be a commentary on the "South Park" controversy.
"I made a cartoon about the television show South Park being censored," she wrote. "I never started a Facebook page. I apologize to people of Muslim faith and ask that this 'day' be called off."
Her cartoon posted at the end of April declared May 20, 2010, as the first annual "Everybody Draw Mohammed Day," and depicts a group of colorful animated objects under the headline: "Will the real likeness of the prophet Mohammed please stand up?!" The cartoon says it is sponsored by "Citizens against Citizens against Humor."
That fictional group now has its own website featuring cartoons and comments.
Attempts to reach Norris for comment were unsuccessful because her telephone number is not listed. Her website has been taken down.
It is not the first time that images of the prophet have sparked anger.
Pakistan and other Muslim countries saw large and sometimes violent protests in 2006 when a Danish newspaper published cartoons of Muhammad, and again in 2008 when they were reprinted. Later the same year, a suspected al Qaeda suicide bomber attacked the Danish Embassy in Islamabad, killing six people.