Deborah Madden, 61, of San Mateo, was indicted on the charge by a federal grand jury last week.
Her plea was entered on her behalf by her lawyer, Paul DeMeester, at today's arraignment before U.S. Magistrate Elizabeth Laporte in San Francisco. Madden did not speak at the hearing.
Laporte informed Madden of the charge and told her that the maximum possible sentence, if she is convicted, is four years in prison.
After prosecutor Andrew Caputo said he didn't oppose allowing Madden to remain free -- but with conditions -- while awaiting trial, Laporte set a hearing on Friday to determine the conditions of release.
Madden will also appear later on Friday before U.S. District Judge Susan Illston, the trial judge assigned to the case, for the setting of future court dates.
Madden's alleged theft of small amounts of cocaine from the lab's drug analysis unit led to the closure of the facility and prosecutors' dismissal of hundreds of criminal cases, among other repercussions.
She admitted to police investigators that she took small amounts of cocaine spilled from evidence on five occasions in 2009.
But Madden was never charged in the state court system with stealing the drug. Late last year, the state attorney general's office said it wouldn't file charges in connection with the alleged laboratory thefts because of a lack of sufficient evidence.
In a separate case, Madden pleaded guilty in San Mateo County Superior Court in June to possessing a small amount of cocaine found in her Peninsula home, and was sentenced to undergo drug counseling.
Outside of court today, DeMeester called the new federal charge "overreaching" and said he doesn't think it applies to Madden's case.
The attorney said he contends that Madden didn't obtain the cocaine by subterfuge or deception.
"The substance was on her desk because that was part of her job," De Meester said.
DeMeester said last week he is considering challenging the federal charge on the ground that it not appropriate for the case.
Madden retired in late 2009 after 29 years on the job as a civilian criminalist with the Police Department.