Investigators say he may have served as the link between the team of hijackers in the United States and senior Qaeda officials in Afghanistan.
He is the second-highest Qaeda official captured in Pakistan.
But officials said that they expected to seek to have some of the senior Qaeda officials executed if convicted.
The so-called high value detainees, the senior Qaeda officials, might not be held at a fixed location, he said, but they were permanently in American custody.
At a minimum, the officials said they believed that other senior Qaeda officials had died in the attack.
Kurdish officials and Ansar defectors have said leaders of the groups that formed Ansar went to Afghanistan in 2000 and 2001 to meet with Qaeda officials.
Asked to list senior Qaeda officials who had been killed, the administration cited six people, four of whom were previously reported to have been dead.
The government has captured several senior Qaeda officials believed to have detailed knowledge of the planning of the attacks and Mr. Moussaoui's role, if any.
In its court filing, the government contends that Mr. Padilla met last year with senior Qaeda officials in Afghanistan and later received explosives training in Pakistan.
One turned out to be Abu Zubaydah, the highest-ranking Qaeda official found since Sept. 11.