U.S. District Judge Ricardo Urbina had thrown out the case in 2009, but an appeals court reinstated the charges last year.
Urbina, who has since retired, said prosecutors built their case on sworn statements the guards had given under a promise of immunity.
A Justice Department attorney told Judge Royce Lamberth yesterday that a special team will ensure that prosecutors working on the new indictment don't have access to "privileged statements."
Prosecutors say they will seek a superseding indictment after gathering additional evidence.
The guards are accused of opening fire in a crowded Baghdad intersection in 2007.
Blackwater is now called Academi. -- AP