During May testimony on Capitol Hill, Comey, who was acting attorney general during Ashcroft's recovery, characterized the move as "an effort to take advantage of a very sick man who did not have the powers of the attorney general."
Comey also noted that senior DOJ officials had legal concerns about the secret program.
But Gonzales shot down Comey's interpretation of the meeting during his testimony last week.
"Mr. Comey's testimony about the hospital visit was about other intelligence activities, disagreements over other intelligence activities," Gonzales said.
The Justice Department and the White House have waved off allegations of perjury, explaining that Gonzales' testimony is "difficult to parse" because of the layers of classified information involved.
"Sometimes it's going to lead people to talk very carefully and there's going to be plenty room for interpretation or conclusion," White House press secretary Tony Snow said in a press briefing last week.
Days after testifying before the Senate it seemed that FBI director Robert Mueller bluntly contradicted Gonzales when he testified before the House Judiciary Committee saying, "The discussion was on a national NSA program that has been much discussed, yes."
Intelligence officials have said the program went outside of the normal review process under the Foreign Intelligence Surveillance Act because of the speed and agility needed to quickly counter threats from al Qaeda. The TSP now operates under the jurisdiction of the secret FISA court.
The discrepancy in Gonzales' and Mueller's testimony appears to be over an NSA data mining project that collected millions of American phone records provided by major phone companies. The government has never publicly acknowledged the existence of the program, which has only been cited by anonymous sources in the media.
Gonzales testified, "The president confirmed the existence of one set of intelligence activities," in reference to the TSP program.
The NSA's data mining project with the phone companies has been the subject of lawsuits against the NSA and AT&T by the American Civil Liberties Union, the Center for Constitutional Rights, the Electronic Frontier Foundation and the Electronic Privacy Information Center. In those cases, submissions and declarations by the director of national intelligence stated the cases sought to expose state secrets.
In a May 13, 2006, declaration by John Negroponte, who was then director of national intelligence, the government maintained, "The purpose of this declaration is to formally assert, in my capacity as DNI and head of the United States intelligence community, the military and state secrets privilege … in order to protect intelligence information, sources and methods that are implicated by the allegations in this case. Disclosure of the information covered by these privileged assertions reasonably could be expected to cause exceptionally grave damage to the national security of the United States and, therefore, should be excluded from any use in this case."