The San Mateo District Attorney's Office filed the charge after police searched Madden's Peninsula home early last month and found a small amount of the drug.
Madden's attorney says she should not be blamed for the problems at the San Francisco crime lab.
"My client has nothing to do with the problems that have historically existed at the crime lab and still exist. The crime lab has been shut down and that's not because of my client," Madden's attorney Paul De Meester said.
The 60-year-old veteran criminalist left the courthouse after posting bail of $10,000. She retired early last month, just before Police Chief George Gascon shut down the drug lab after investigators said she had stolen cocaine evidence late last year.
That investigation continues and no charges have been filed in that case. Since then, the district attorney's office has dropped about 500 drug cases where evidence may have been compromised.
Coincidentally, while Madden was in court, prosecutors dropped about a dozen more cases on Monday morning at San Francisco's Hall of Justice.
But district attorney spokesman Brian Buckelew says his office has now identified a large number of cases they can salvage.
"For instance, the defendant has a number of priors for the same activity. Those priors can come into evidence. You're talking about cases with confessions," he said.
Add a new wrinkle to all this -- police have discovered a large army of feral cats living near the lab around a property room where old evidence is stored. There is concern they may be feasting on some of that evidence.
"The latest story about these feral cats being in there, I mean what's going to be next? You're going to have a circus marching out of there," Jeff Adachi said.
Police officials say they're removing the cats in a humane way with the assistance of the city's Animal Care and Control agency.
The district attorney's office told ABC7, there is now a backlog of about 400 fresh cases which have never had their drug evidence tested and they can only get 15 cases tested in a day in those outside labs
In the meantime, that backlog keeps growing.