BOSTON (WHDH) -- Two employees at a state crime lab are out of a job as a result of an investigation that led to the shutdown of the crime lab after allegations of evidence tampering.

State officials announced on Thursday the former director of the lab resigned and the director of the analytical chemistry division was fired. A third person, who had direct authority over the chemist involved, could be fired.

State police, who recently took over the lab, said a chemist violated testing protocols and may have deliberately mishandled drug samples. State officials are probing the chemist who resigned in March. She could face criminal prosecution.

“There were several red flags that should have been noted and prompted closer scrutiny and earlier actions, but these flags were either missed or ignored,” said Health and Human Services Secretary JudyAnn Bigby.

Police said the former chemist apparently took at least 90 samples relating to Norfolk County drug cases without having an evidence officer sign them out, as protocol requires. Her motive is unknown.

“She has admitted to some malfeasance and that will be an ongoing investigation, part of the attorney general’s investigation,” said Dept. of Public Safety Secretary Mary Elizabeth Heffernan.

The former chemist handled over 60,000 drug samples relating to more than 40,000 cases, many more than her colleagues, but it appears she received no extra compensation for handling so many.

In a 2010 trial she testified, “I run the quality control/quality assurance within the drug lab.” Officials said they are trying to find out if that is true.

“I think that if she was in control in that lab then the problem is a lot bigger than the cases she herself tested,” said Criminal Defense Attorney Rosemary Scapicchio.

Officials do not know how far-reaching this is.