"We were involved in a search," said FBI spokeswoman La Rae Quy. "The supporting documents for the search are sealed."
Local media reported that one reason for Wednesday's search was related to a federal probe of leaks of grand jury testimony.
Reports in the San Francisco Chronicle on the testimony by top athletes prompted the attorney for Barry Bonds to admit last month that the baseball legend had used creams and oils that could have contained steroids, but had done so unknowingly out of blind faith in his trainer.
Conte's attorney, Robert Holley, said he would respond to the search with a new legal filing.
Conte's motivation to seek a plea deal increased after he confessed in an article and television interview last month that he did distribute steroids as charged.
The BALCO case has soiled the reputations of top athletes including Bonds and sprint champion Marion Jones, who recently sued Conte for defamation.