Lt. Gen. Stanley McChrystal, who was head of the military's Joint Special Operations Command at the time and approved the paperwork awarding Tillman a Silver Star, had been accused by Tillman's family of covering up the circumstances of his death.
McChrystal on Tuesday said the handling of the matter was "well-intentioned" but admitted that the Silver Star award caused some misunderstanding.
"It still produced confusion at a tragic time, and I'm very sorry for that," McChrystal said during his confirmation hearing before the Senate Armed Services Committee. He earlier expressed his "deepest condolences" to Tillman's family and fellow rangers.
McChrystal said he did not read the Silver Star citation well enough, and admitted that the language in the citation implied that Tillman was killed by enemy fire. He suggested the citation was prepared and written in haste.
"I would do this differently if I had the chance again ... in retrospect they look contradictory," he said.
McChrystal said there was speculation early on that Tillman was killed by friendly fire, but that he and others were waiting for the outcome of an "initial review" before coming forward with that information.
"It was a well-intended intent to get some level of proof before we went out," he said.
McChrystal said the nature of Tillman's death did not in any way make the Silver Star inappropriate. He said Tillman "absolutely" earned the award.
Shortly after McChrystal was named to replace Gen. David McKiernan in Afghanistan, Pat Tillman Sr. told The Associated Press that he still believes McChrystal "participated in a falsified homicide investigation."
McChrystal also answered questions Tuesday on Capitol Hill about the use of interrogation techniques like sleep deprivation, stress positions and use of dogs under his watch.
He said some, but not all, of those techniques were used, but that interrogators began to "reduce" the use of such methods and that he was not comfortable with them.
McChrystal said he followed guidelines and investigated any allegations of abuse.
"I do not and never have condoned mistreatment of detainees and never will," he said.