Bonds, 44, is due to go on trial in March in the court of U.S. District Judge Susan Illston on charges of making false statements and obstructing justice in 2003 grand jury testimony in a sports steroids probe.
The former San Francisco Giants slugger is accused of lying when he denied ever receiving anabolic steroids or human growth hormone.
In a pretrial ruling, Illston granted a request by Bonds' six defense lawyers for dismissal of five of the false statements counts on the grounds they were legally defective.
The judge found that two counts duplicated other counts, two were based on ambiguous questions or answers and one other charge contained a typo in which prosecutors left out a key word.
But the judge turned down Bonds' request for dismissal of five other counts.
The ruling still leaves Bonds facing 10 criminal counts, each of which carries a potential maximum sentence of five years in prison. In addition, prosecutors have said they plan to seek a new indictment correcting the charge in which a word was left out, which would bring the total number of counts to 11.
If Bonds is convicted, however, the actual penalty would be determined under federal sentencing guidelines and is expected to be lower than the maximum five years.
Last month, Illston sentenced two other sports figures who were convicted of lying in the steroids probe to home confinement or probation.
Bonds, now a free agent, set the Major League Baseball record for career home runs while playing for the Giants last year.