The indictment against Jared Loughner, 22, accuses him of attempting to assassinate Giffords and trying to kill two of her aides.
Those are potential death penalty charges. A statement from the U.S. attorney for Arizona, Dennis Burke, said those require a more painstaking process under Justice Department rules.
Burke said the initial indictment issued by a grand jury in Tucson was just the beginning of federal legal action against the 22-year-old Tucson resident.
Six people were killed and 13 wounded in the Jan. 8 attack at a grocery store in Tucson as Giffords held a meet-and-greet with constituents. State charges are pending.
Calls to each of Loughner's attorneys, Judy Clarke and Mark Fleming, weren't immediately returned Wednesday evening.
The indictment was expected. The federal criminal code mandates that an indictment be brought within 30 days of an arrest.
Before federal officials seek charges carrying the death penalty, families of the victims will be consulted and a review by a Justice Department committee is required.
Loughner remains in federal custody without the possibility of bond. He is set for a preliminary hearing on Monday in Phoenix.
The San Diego-based judge set to hear the case ordered it moved to a larger federal courtroom on Wednesday. The courtroom is the centerpiece of the downtown Phoenix courthouse and is mostly used for ceremonial and high-profile hearings.