A federal grand jury in Miami indicted Padilla and four others.
While the charges allege Padilla was part of a US-based terrorism conspiracy, they do not include the government's earlier allegations that he planned to carry out attacks in the United States.
"The indictment alleges that Padilla travelled overseas to train as a terrorist with the intention of fighting a violent jihad," Attorney General Alberto Gonzales said at a news conference in Washington.
Gonzales declined to comment on why none of the allegations involving attacks in America were included in the indictment.
Padilla, a US-born Muslim convert, has been held as an "enemy combatant" in military custody for more than three years.
Padilla faces life in prison if convicted on the three charges, one count each of conspiracy to murder, maim and kidnap people overseas, providing material support to terrorists and conspiracy.
Gonzales said the case would go to trial in September 2006.
The indictment avoids a Supreme Court showdown over how long the US government could hold one of its citizens in military custody without charges.
Padilla's lawyers had asked justices to review his case last month, and the Bush administration was facing a deadline next Monday for filing its legal arguments.
Padilla was arrested at Chicago's O'Hare International Airport in 2002 after returning from Pakistan.
The charges against him and four others allege they were part of a North American support cell that sent money, assets and recruits overseas "for the purpose of fighting violent jihad".
The indictment mentions Afghanistan, Bosnia, Chechnya, Egypt and Bosnia, but makes no allegations of specific attacks anywhere.
The others indicted are: Adham Amin Hassoun, a Lebanese-born Palestinian who lived in Florida; Mohammed Hesham Youssef, an Egyptian who lived in Florida; Kifah Wael Jayyousi, a Jordanian national and US citizen who lived in San Diego; and Kassem Daher, a Lebanese citizen with Canadian residency status.
Hassoun and Jayyousi are in federal custody in Miami, while Youssef is serving a prison sentence in Egypt, Justice Department officials said.
Daher is believed to be in Lebanon, but officials said they are uncertain whether he is in custody.