Two Pulitzer Prize-winning New York Times journalists are under scrutiny for their involvement in top-secret military missions that critics say compromised their reporting during a time of war.

One is reporter Judith Miller, who claimed in an article to have told the special counsel investigating the alleged leak of a CIA agent’s identity that she had security clearance while hunting for weapons of mass destruction in Iraq with a U.S. Army unit.

Ms.Miller’s claim prompted a retired CBS News correspondent, Bill Lynch, to write in a letter to the journalism Web site Poynter.org that the security clearance came “as close as one can get to government licensing of journalists.”

The second case is only beginning to catch the public eye – perhaps because it’s nearly 60 years old. It involves what some say is the most impressive scoop in journalistic history, science writer William Laurence’s 10-part series on the making of the atomic bomb and his eyewitness account of the bombing of Nagasaki, Japan.

In order to get the story, Laurence agreed to serve as a secret consultant to the Manhattan Project, chronicling the development of the bomb for President Truman and Secretary of War Stimson. After the atomic bombs were dropped, the Times on August 7, 1945, disclosed in a short article that its reporter “obtained leave from this newspaper at the War Department’s request to explain the intricacies of the atomic bomb’s operating principles in laymen’s language.”

A month later, the Times published Laurence’s account of flying in a B-29 over Nagasaki, a half-mile behind the plane that dropped the weapon. He described the mushroom cloud as “seething and boiling in a white fury of creamy foam.”

Two months ago, two journalists started a campaign to have Laurence stripped of his 1946 Pulitzer Prize for his account of the Nagasaki bombing and for his subsequent articles on the atomic bomb.

Behind the campaign are a liberal radio host,Amy Goodman, and her brother, David Goodman, a freelance writer, who claim that Laurence’s reporting on the radiation effects of atomic weapons amounted to government propaganda. In both Ms. Miller’s case and Laurence’s, “they are parroting the government line,” Ms. Goodman told The New York Sun in a telephone interview.

The story by Laurence they are most critical of is a piece headlined “U.S. Atom Bomb Site Belies Tokyo Tales,” in which he cast doubts on Japanese claims that radiation caused casualties in Japan in the days after the explosions.That article was not among those submitted to the Pulitzer Prize board.

The administrator of the Pulitzer Prize at Columbia University, Sig Gissler, said the board had received the request from the Goodmans. “We give complaints appropriate attention,” he said.

Unlike Ms. Miller, who is accused of writing overly optimistic reports about progress made by the 75th Exploitation Task Force unit in Iraq, Laurence “had no real-time effect on policy,” said James Fallows, a national correspondent for the Atlantic Monthly magazine and author of a series of articles critical of the Bush administration’s planning and execution of the war. Laurence, he pointed out, wrote during a time when every American institution, including the press, was involved in the war effort.

It’s not clear whether Ms. Miller actually had an official security clearance or whether she had a less formal agreement with the military that she would keep secret classified information she came across while with the unit in 2003.

In the beginning of July, days before she was temporarily jailed for for contempt of court, her lawyers filed a court document containing a letter written by high-ranking members of her weaponshunting unit who said she was “routinely exposed to secret information, which if compromised could have endangered both operational and national security. Ms. Miller would never reveal what she learned, how she learned it, or from whom she learned it.”

The letter, dated February 14, 2005, did not specify whether she had a special security clearance that would have involved a thorough background check. All reporters embedded with military units in Iraq were required to sign agreements not to disclose classified information.

Pentagon officials said they could not disclose the identity of people possessing security clearance or the level of the clearances.

A spokeswoman for the Times, Catherine Mathis, did not return calls seeking comment on Ms. Miller’s security clearance.