Instead, U.S. District Judge Marcia Cooke ordered all defense lawyers in the case to sign papers indicating they understood and would follow rules barring disclosure of certain evidence.
Cooke also said she might hold in contempt anyone who receives such prohibited material, and she specifically mentioned several reporters attending Wednesday's hearing.
"The lash is about to fall on all," Cooke said. "We're going to have a trial, as much as possible as we can, a trial on the evidence, and not on anything else."
The leaked transcripts documented seven telephone conversations on which Padilla's voice is heard that were intercepted under the Foreign Intelligence Surveillance Act. Defense lawyers have said that Padilla is never overheard discussing any violent acts and that many of the conversations involve family matters, casting doubt on the strength of the government's case.
The transcripts are not classified but were covered under Cooke's order barring disclosure.
Michael Caruso, one of three Miami-based public defenders on Padilla's defense team, acknowledged that one of them was responsible for providing the material to The New York Times, which published the story Jan. 4.
The leaker was identified in a sealed court filing to Cooke, but it was not made public and none of the lawyers would name the person responsible.
"This was a simple misunderstanding, an honest mistake, and it has been rectified," Caruso said. "Your honor can rest assured that this matter is at an end. There have been no further disclosures."
Prosecutors had wanted Cooke to begin a formal investigation of the disclosure.
"What was the point? It was clearly calculated to influence the jury of public opinion and try this case there," Assistant U.S. Attorney Brian Frazier said. "It was a deliberate violation."
The Times has declined to comment.
Padilla, 36, is accused along with two others of being part of a North American cell that provided cash, supplies and recruits to Islamic extremist causes worldwide. Padilla, a U.S. citizen, was accused after his 2002 arrest of being on an Al Qaeda mission to detonate a radioactive "dirty bomb" in a major U.S. city, but those allegations are not part of the Miami case.
Padilla was held without charge for 3 1/2 years at a Navy brig after President Bush designated him as an enemy combatant. He was added to the Miami case in late 2005 amid an escalating legal battle over the president's powers to indefinitely detain Padilla and others during wartime.
Padilla and his co-defendants have pleaded not guilty. Trial is scheduled to begin April 16, and that could hinge on whether Padilla is found competent. His lawyers say he is suffering mental problems stemming from his long, isolated military confinement.Click here for FOXNews.com's War on Terror Center.