SAN FRANCISCO — The government’s lead sports doping investigator and several other Internal Revenue Service agents have been cleared of any wrongdoing in a raid on the home of Barry Bonds’ personal trainer.

When federal agents raided the home of Bonds’ trainer, Greg Anderson, on Sept. 3, 2003, they seized $63,920 from a safe and a drawer in his kitchen. Less than a month later, $600 went missing, and several IRS agents, including BALCO investigator Jeff Novitzky, were placed under investigation.

According to court documents filed Thursday, the IRS’ yearlong internal investigation concluded that “it did not identify who was responsible for taking the missing $600.”

But the investigation has become an issue in Bonds’ upcoming trial and in the case of cyclist Tammy Thomas, who was convicted last year of lying to a grand jury when she denied using steroids.

U.S. District Judge Susan Illston ordered prosecutors last week to turn over the 136-page IRS report to Bonds’ attorneys. Whether they can or will use the report to cross examine Novitzky when he testifies for the government remains to be seen.

Bonds’ lead attorney Allen Ruby declined comment.

Illston barred Thomas’ attorney from questioning Novitzky about the investigation during her April 2008 trial. The judge ruled the raid on Anderson’s house had nothing to do with the cyclist’s case, though she said it might have been relevant in the original BALCO criminal case that charged Anderson, BALCO founder Victor Conte and two others with steroids dealing. Anderson, Conte and the others pleaded guilty in 2005 before their cases went to trial.

Thomas’ attorney Ethan Balogh recently was given a copy of the full report by the prosecution. In a motion Thursday, he said he was provided with an incomplete synopsis of the IRS internal investigation before the start of the cyclist’s April 2008 trial. His filing seeking permission to share the report with his client included a copy of the document.

Although the synopsis mentioned missing money, Balogh said it did not contain information that the IRS investigated allegations in the media that Novitzky was targeting Bonds for personal reasons and that he planned to write a book about the BALCO investigation.

Novitzky told the IRS agent investigating him that any comments about a book deal “could have been a misconstrued comment that was made as a joke and overheard incorrectly by others,” according to the IRS report.

Novitzky was cleared of those allegations as well.