The indictment in U.S. District Court for Northern California in San Francisco charged Tammy Thomas, 36, with three counts of perjury and one count of obstruction of justice.
A silver medallist in the sprint competition at the 2001 World Championships, Thomas was banned for life from the sport in August 2002 after testing positive for Norbolethone, an anabolic agent.
The federal indictment against her says she lied when she told the grand jury in 2003 she never used performance- enhancing drugs.
"Perjury undermines the fundamental mission of our investigative and judicial processes - to uncover the truth," U.S. Attorney Kevin Ryan said in a statement. "Lying under oath to a grand jury must be vigorously prosecuted, or else this essential truth-finding mission is significantly undermined."
A woman who answered the phone at Thomas' parents' home in Mississippi said she was not available for comment. Thomas, who is set to appear in court on Jan. 5, also did not return a message for her left on a cell phone voice mail system.
The indictment shows federal prosecutors are still following up on the high-profile BALCO case that has tarnished some of the top names in track and field, baseballand football.
Federal officials are also investigating whether baseball superstar Barry Bonds lied when he testified before the federal grand jury in a case that led to the imprisonment of his personal trainer and the head of the San Francisco-area BALCO nutritional lab.
Bonds, who holds second place on the Major League Baseball career home-run list, told the grand jury he never knowingly used steroids. The San Francisco Giants last week agreed to pay the 42-year-old slugger $16 million to play next year in a season when he hopes to become the all-time home-run king.
The latest indictment against Thomas said she also lied when she said she did not obtain illegal performance-enhancing drugs from Patrick Arnold, who has since been convicted in the BALCO case. Arnold was credited with creating the previously undetectable steroid THG.
"In the early stages of the investigation, the individuals who distributed steroids to some of the nation's top-flight athletes were indicted and convicted," Ryan said. "In the second stage, we developed the evidence to indict and convict the creator of the undetectable steroid THG distributed through BALCO."
"A third stage has begun as we bring charges against individuals who lied to investigators or committed perjury while testifying under oath to a federal grand jury. Our investigation into each of these stages will continue as the evidence develops."