Department spokesman Bryan Whitman said Charles "Cully" Stimson, deputy assistant secretary of defense for detainee affairs, told him on Friday that he had made his own decision to resign and was not asked to leave by Defense Secretary Robert Gates.
Stimson said he was leaving because of the controversy over a radio interview in which he said he found it shocking that lawyers at many of the nation's top law firms represent detainees held at the U.S. military prison in Cuba.
"He believed it hampered his ability to be effective in this position," Whitman said of the backlash to Stimson's comments.
Stimson drew outrage from the legal community — and a disavowal from the Defense Department — for his Jan. 11 comments, in which he also suggested some attorneys were being untruthful about doing the work free of charge and instead were "receiving moneys from who knows where."
He also said companies might want to consider taking their legal business to other firms that do not represent suspected terrorists.
"I think, quite honestly, when corporate CEOs see that those firms are representing the very terrorists who hit their bottom line back in 2001, those CEOs are going to make those law firms choose between representing terrorists or representing reputable firms," Stimson told Federal News Radio.
Stimson publicly apologized several days after the radio interview, saying his comments did not reflect his values and that he firmly believes in the principles of the U.S. legal system.
But it didn't completely quiet critics.
The Bar Association of San Francisco last week asked the California State Bar to investigate whether Stimson violated legal ethics by suggesting a boycott of law firms that represent Guantanamo Bay detainees.