P.J. Crowley told the BBC's "HARDtalk" program the alleged harsh treatment of the accused WikiLeaks source was undermining his "legitimate" prosecution.
Manning is in solitary confinement in Quantico, Va., under conditions his supporters call cruel and abusive.
"I thought the treatment of Bradley Manning was undermining what I considered to be a very legitimate prosecution of an individual who has profoundly affected U.S. national security," Crowley said in his first public statement since resigning March 13. He declined to say whether he was fired.
Crowley said he did not anticipate the military's fierce reaction to his remark that Manning's treatment was "stupid." He said it was appropriate for him to quit because he had put President Barack Obama in a "difficult position."
"Quite honestly, I didn't necessarily think the controversy would go as far as it did. but I don't regret saying what I said," he said.