Padilla, who is being held at the Navy brig near here, filed a complaint in U.S. District Court here after the U.S. Supreme Court in a narrow ruling last week decided Padilla's original case should not have been brought in federal court in New York, his attorney Donna Newman said.
"We have to just move forward. It's just a matter of time now," said Newman, who filed the lawsuit Friday.
The justices, in a June 28 decision, ruled the New York court did not have legal authority over the brig's commander, Melanie Marr, who was named in the original suit.
The Brooklyn-born suspect initially was held as a material witness in the investigation following the Sept. 11, 2001, terrorism attacks. Within days the government designated him an enemy combatant and he was moved to the brig near here and prevented from challenging his detention.
Attorneys for Padilla later sued and, last December, the U.S. 2nd Circuit Court of Appeals in New York City ordered him released from military custody within a month unless the government chose to charge him.
That ruling was suspended until the Supreme Court considered the case.
The U.S. administration considers some terror suspects enemy combatants and says they could be held indefinitely without charge.
The justices did not address the broader question of whether President Bush had congressional authority to designate Padilla an enemy combatant or whether indefinite detention without charges or trial violated his constitutional rights.
Padilla, described by authorities as a former Chicago gang member, is being held amid allegations he sought to detonate a "dirty bomb" and blow up apartment buildings in the United States.
The government said he proposed the idea to a top al Qaeda terrorism coordinator who has since been arrested in Pakistan.
In a dissent to the Supreme Court decision, Justice John Paul Stevens argued Padilla was an "exceptional case" that warranted the Supreme Court's jurisdiction and a ruling on whether detention was lawful.
The FBI arrested Padilla in May 2002 as he returned from a trip to Pakistan.
In a related case, the Supreme Court ruled that Mr. Bush had the right to imprison another enemy combatant, Yaser Hamdi, but that Hamdi had the right to counsel and to challenge his detention in court.
In a second ruling, the justices said that terrorism suspects held at Guantanamo Bay must have court hearings as well.
Last month, The Justice Department detailed Padilla's alleged al Qaeda training in Afghanistan and contacts with the most senior members of the terrorist network, his travel back into the United States and preparations to rent apartments and set off explosives.
The government said Padilla sought to blow up hotels and apartment buildings in the United States in addition to planning an attack with a "dirty bomb" radiological device.
Deputy Attorney General James Comey called the chronicle of Padilla's plotting "remarkable for its scope, its clarity and its candor."
The department released documents, based in part on interviews with Padilla, saying he and an unidentified al Qaeda accomplice planned to find as many as three apartment buildings supplied with natural gas.
"Padilla and the accomplice were to locate as many as three high-rise apartment buildings which had natural gas supplied to the floors," the government summary of interrogations said. The alleged accomplice is in custody.
"They would rent two apartments in each building, seal all the openings, turn on the gas, and set timers to detonate the buildings simultaneously at a later time," the papers alleged.
Comey said Padilla suggested to his handlers that he detonate a nuclear bomb that he thought he could make from instructions on the Internet, or that he set off a dirty bomb that would release deadly radiation in a small area. His handlers did not think either was feasible, Comey said, and wanted him to focus instead on the apartment-building plot.
Top al Qaeda officials "wanted Padilla to hit targets in New York City, although Florida and Washington, D.C. were discussed as well," the summary said.
One of Padilla's lawyers, Andrew Patel, characterized Comey's information as "an opening statement without a trial."