John Walker Lindh, 24, from California, was captured in 2001 and jailed for 20 years under a plea deal.
His father Frank Lindh told the Commonwealth Club in San Francisco: "The maltreatment and imprisonment of John Lindh was - and is - a human rights violation.
"It was based purely on an emotional response to the 9/11 attacks, not on an objective assessment of the facts of John's case."
US troops overthrew Afghanistan’s Taliban government after it refused to hand over al-Qaida leader Osama bin Laden.
At times fighting back tears, the father accused US forces of torturing his son. He showed a photo of his son's body strapped to a stretcher at a military base in southern Afghanistan.
"I do not want to dwell today on the military's mistreatment of my son, but I will say categorically that he was treated in a way that is shameful to our nation and its ideals," said Lindh, an attorney at Pacific Gas & Electric.
"He was treated in a way that is shameful to our nation and its ideals"
"John Lindh did not need to be tortured to tell the American forces where he had been and what he had seen," the father said. "I cannot fathom why the military felt it necessary to humiliate him in this way."
Reviled by many Americans as a traitor, Lindh agreed to a plea deal in which he was spared a possible life prison sentence and all terrorism charges against him were dropped.
In exchange, he pleaded guilty to two charges of aiding the Taliban and carrying explosives. Now in federal prison in southern California, John Walker Lindh is appealing to George Bush, the US president, to commute his sentence.
Frank Lindh said he was proud of his son.
"He was extremely unpopular in the United States and probably still is because of the way his case was portrayed by the government and by the media," he said. "People will come to realise that what happened in his case was wrong, that the torture was wrong."