The ruling removes one of the last major obstacles to the start of Padilla's trial next week.
U.S. District Judge Marcia Cooke stressed in a 12-page order filed late Monday that she was not passing judgment on the torture allegations. Rather, she said the effort to dismiss the case for "outrageous government conduct" was faulty on legal grounds.
Padilla's lawyers claim that during the 3½ years the former Chicago gang member was held as an "enemy combatant" at a Navy brig he was routinely subjected to harsh treatment and torture.
He claimed that he was forced to stand in painful stress positions, given LSD or some other drug as a "truth serum," subjected to loud noises and noxious odors, and forced to endure sleep deprivation, extreme heat and cold and harsh lights.
The Pentagon and Justice Department have repeatedly denied those claims. Officials with the brig in Charleston, S.C., said during earlier testimony before Cooke that Padilla, a 36-year-old U.S. citizen and Muslim convert, was not mistreated, though they acknowledged occasional removal of the mattress in his cell and of his copy of the Quran.
Padilla and his co-defendants, Adham Amin Hassoun and Kifah Wael Jayyousi, are scheduled for trial starting next Monday.
The three are charged with conspiracy and terrorism material support for allegedly being part of a North American support network for Islamic extremist groups worldwide. All three have pleaded not guilty and could face life in prison if convicted.
In her ruling on the dismissal motion, Cooke said Padilla's attorneys failed to back up their claims with adequate case law. She said the motion also failed on legal grounds because prosecutors aren't using any evidence collected during Padilla's time in the brig.
She warned, however, that the issue could return should prosecutors decide to use evidence from Padilla's interrogations.
Cooke had ruled earlier that Padilla was competent to stand trial despite conclusions from defense mental health experts that he was suffering from post-traumatic stress disorder stemming from his years in military custody.
Padilla was initially arrested in 2002 on suspicion of an al Qaeda plot to detonate a radioactive "dirty bomb" in a U.S. city, but that charge is not part of the Miami criminal case. Prosecutors claim that Padilla filled out a form in 2000 to join an al Qaeda training camp in Afghanistan.