When it published the article, the newspaper reported that it had delayed publication because the George W. Bush White House had argued that publication "could jeopardize continuing investigations and alert would-be terrorists that they might be under scrutiny." The timing of the New York Times story prompted debate, and the Los Angeles Times noted that "critics on the left wondering why the paper waited so long to publish the story and those on the right wondering why it was published at all." Times executive editor Bill Keller denied that the timing of the reporting was linked to any external event, such as the December 2005 Iraqi parliamentary election, the impending publication of Risen's book State of War: The Secret History of the CIA and the Bush Administration, or the then-ongoing debate on Patriot Act reauthorization. Risen and Lichtblau won the Pulitzer Prize for National Reporting in 2006.

In an interview in 2013, Keller said that the newspaper had decided not to report the piece after being pressured by the Bush administration and being advised not to do so by The New York Times Washington bureau chief Philip Taubman, and that "Three years after 9/11, we, as a country, were still under the influence of that trauma, and we, as a newspaper, were not immune."