Annie Dookhan was arraigned on the charges in Suffolk Superior Court, and faces an additional 12 in other counties. She was indicted by a grand jury on Tuesday.
State prosecutors allege Dookhan fabricated test results and tampered with drug evidence in testing substances for criminal cases. Judges have released about 200 defendants from custody in the last few months and put their cases on hold. The state also is reviewing thousands of other cases possibly affected by Dookhan's work.
Dookhan, 35, pleaded not guilty to one count of perjury, five counts of obstruction of justice, one count of making a false claim of holding a master's degree and eight counts of evidence tampering.
The Franklin resident, who was released on $10,000 bail following her arrest in September, was given one small allowance Thursday when Magistrate Judge Gary Wilson agreed to lengthen the time she can spend outside her home. The judge changed her curfew from 6 p.m. to 10 p.m. She must continue to wear a GPS tracking device.
Dookhan did not speak with reporters after her arraignment. Her lawyer, Nicolas Gordon, said it was too early for him to comment because he has yet to review much of the evidence.
Attorney General Martha Coakley said after the indictments were returned that Dookhan's actions "have sent ripple effects throughout the criminal justice system."
State police shut down the lab in August. Many more than the 200 cases that were put on hold since then could be affected because authorities say Dookhan tested more than 60,000 samples involving 34,000 defendants during her nine years at the lab.
During her initial arraignment in September, Assistant Attorney General John Verner said state police learned of Dookhan's actions after a chemist at the lab said he observed "many irregularities" in Dookhan's work.
Verner said Dookhan later acknowledged to state police that she sometimes would test only five out of 15 to 20 samples but would list them all as positive for the presence of a drug. She also allegedly acknowledged that sometimes, if a sample tested negative, she would take known cocaine from another sample and add it to the negative sample to make it test positive.
The only motive authorities have described is that Dookhan wanted to be seen as a good worker.
Dookhan was suspended from lab duties after she allegedly was caught forging a colleague's initials in June 2011. She resigned in March during an internal investigation by the Department of Public Health. Amid that investigation, state police took over the lab in July as part of a state budget directive.