BOSTON (WHDH) -- Massachusetts Public Health Commissioner John Auerbach resigned in the wake of a growing investigation into a chemist whose alleged mishandling of drug samples led police to shut down the state crime lab.

Auerbach said what happened at the lab was unacceptable and the buck stopped at his office.

"It is clear that there was insufficient quality monitoring, reporting and investigating on the part of supervisors and managers surrounding the former Department of Public Health drug lab in Jamaica Plain - and ultimately, as Commissioner, the buck stops with me,” Auerbach said in a statement.

Governor Deval Patrick accepted Auerbach’s resignation.

“He identified areas where things could have been done different, where there was a breakdown in management and that there were some things that should have raised red flags that were missed. And again, he accepted responsibility for that,” said Judyann Bigby, secretary of health and human services.

Auerbach's decision comes as prosecutors start the process of figuring out how to deal with tens of thousands of drug cases handled by the chemist.

State police closed the lab late last month after discovering that the chemist had failed to follow testing protocols and may have purposely mishandled key evidence.

The Associated Press contributed to this report.