Lehnert, 58, was commander of Joint Task Force 160 when it was assigned to build prison cells in 2001 at the U.S. Navy base in Cuba to hold designated "enemy combatants" from Afghanistan and elsewhere.
He said he was given little guidance from the Pentagon, but he did have his staff read the Geneva Convention, the international agreement governing treatment of prisoners.
"I wanted to run it close to Geneva Convention rules," Lehnert said. "Our job was to take them out of the fight, and once we had done that, I felt we had a moral responsibility to take care of them."
However, another task force was put in charge of interrogating detainees, and there were disagreements over their treatment, Lehnert said.
"I think it is extraordinarily important how we treat prisoners," he said. "Obviously, there were other views."
"I came to the conclusion very soon that this probably wasn't the right way to go," said Lehnert, who served just 100 days at the base.
"Probably before I left Guantanamo, I was of the opinion it needed to go away as soon as possible," he said.
The general said he didn't feel the U.S. would get much useful information by using the techniques.
"I think we lost the moral high ground," he said.
President Barack Obama has ordered the prison to close by January 2010, but it's unclear where about 200 remaining prisoners would go.