Bonds is charged with four counts of perjury and one count of obstruction for allegedly lying 19 different times during his December 2003 testimony to a grand jury investigating steroid use in professional sports.
The indictment, unsealed in November, cites snippets of testimony where Bonds denies ever ingesting steroids or human growth hormone. It quotes Bonds denying his personal trainer Greg Anderson ever injected him with steroids, which prosecutors allege is a lie.
During his grand jury appearance, prosecutors also presented Bonds with a drug test showing a positive steroids result for a player they called "Barry B." Bonds said he never before saw those results.
U.S. District Court Judge Susan Illston made the ruling on the testimony Friday when she ordered federal prosecutors to fix Bonds indictment so each of the five counts against him don't include multiple alleged false statements.
The indictment cites 19 different instances of Bonds' alleged lying but only charges him with four counts of perjury and one count of obstruction.
Illston agreed with Bonds' attorney Dennis Riordan that prosecutors must edit out many of the alleged lies or seek a new indictment containing more charges.
Prosecutors are expected to make their decision before Bonds' next court date on March 21. They declined comment outside court.
The judge allowed Bonds to skip the hearing Friday and excused him from attending the next court date.