Auerbach, a popular fixture in public health agencies for more than two ­decades, described what happened at the Jamaica Plain lab as unacceptable. He pledged after his departure to continue working with investigators frantically trying to unravel the extent of the evidence mishandling, which may have been going on for years.

“Ultimately, as commissioner, the buck stops with me,” John Auerbach, the state’s public health chief for 5½ years, said in a statement.

An unfolding scandal at a state laboratory is forcing the resignation of the top Massachusetts public health official, who said Monday that he bears ultimate responsibility for a lack of oversight that led to mishandling of drug evidence, possibly jeopardizing thousands of criminal cases.


The Globe reported that internal ­e-mails from chemists and supervisors at the drug laboratory ­describe a staff drowning in work, instances of misplaced evidence in crime cases, and mounting frustration over the Patrick administration’s seeming indifference.

One of the e-mails pointed out that a supervisor had scheduled a meeting in 2008 to discuss the lab’s problems with Auerbach.

“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,” Auerbach said in his statement.

A chemist who worked there for nine years, Annie Dookhan, stands at the center of the crisis, which prompted the firing of one lab supervisor and the resignation of the executive who supervised all the labs in a sprawling complex.

Even the union that represents the chemists who worked at the troubled state crime lab had kind words for Auerbach, who earned $146,633 annually. Auerbach has accepted the post of director of Northeastern University’s Urban Health ­Research Institute; he will also be a professor there.

“Commissioner Auerbach’s career and accomplishments . . . should not be discounted as a result of this present issue,” Joe Dorant, president of the Massachusetts Organization of State Engineers & Scientists, said in a statement.


It’s “not unlike the 12 other scientists and chemists — representing more than 200 years of education and experience and who work each and everyday to keep our Commonwealth safe — who should not be ­penalized for the alleged activities of one employee,” Dorant said.

Appointed commissioner in 2007, Auerbach was hailed Monday by health advocates, academics, and elected officials for his pioneering work and passion in serving the state’s most vulnerable residents.

Auerbach will continue to stay in the position for a few weeks until a successor is named, according to a Patrick administration official.

Governor Deval Patrick said in a statement that problems uncovered at the lab are “deeply troubling” but are not representative of Auerbach’s work or of the rest of his department.

“It saddens me to accept his resignation,” Patrick said.

Investigators say that Dookhan mishandled drug samples, by altering the weight of the drugs, not calibrating machines correctly, and manipulating samples so that they would test as drugs when they were not.

State Police have notified prosecutors that Dookhan may have handled 60,000 drug samples, representing 34,000 criminal cases, and some or all of the evidence may be tainted. Dookhan resigned in March.

Officials say the problems with Dookhan were not discovered until June 2011. Auerbach was not alerted until six months later, according to a timeline released last week by the Patrick administration. District attorneys and State Police were not made aware of the full gravity of the situation until months later.


Auerbach’s resignation statement fails to shed light on why several months passed from the time he became aware of problems at the lab and when law enforcement authorities were notified.

Mayor Thomas M. Menino of Boston, who tapped Auerbach to run the city’s health agency in the 1990s, said he called Auerbach early Monday to urge him to “keep your head up.” Auerbach told the mayor he was resigning.

“For all the wonderful things he did over the years, his career should not be blemished by this one incident,” Menino said. “Every­thing I know about public health John Auerbach taught me.”

As Boston’s health chief, he formed a coalition of cities and towns that in short order enacted smoking bans in restaurants and bars, setting the stage to win legislative approval for a long-stalled statewide prohibition.

During an earlier stint at the Public Health Department, as an assistant commissioner, he oversaw the HIV/AIDS Bureau. He was recognized as one of the few openly gay men in high government positions.

Kara Suffredini, executive director of MassEquality, which lobbies for the rights of gay, lesbian, bisexual, and transgender residents, said when Auerbach was appointed public health commissioner, he traveled the state listening to the gay community after years of strained relations under Patrick’s predecessor, Mitt Romney.

She said Auerbach’s department released an antibullying guide, suppressed earlier by the Romney administration, with advice for schools and health professionals on how to help lesbian, gay, bisexual, and transgender students be safer in schools.


As state health commissioner, Auerbach oversaw an agency with thousands of employees, and that includes four public health hospitals, the State Laboratory, and divisions that deal with chronic and infectious disease, substance abuse, environmental health, tobacco control, child and adolescent health, and emergency preparedness. Auerbach was the face of government during health crises such as the arrival of swine flu in 2009.

For the legions of local health workers who inspect restaurants, hold flu clinics, and perform dozens of other jobs, he was a leader who understood the burden of too much work and not enough money, public health advocates said.

“He listens,” said Thomas Carbone, public health director in Andover and immediate past president of the Massachusetts Health Officers Association, a trade group representing health workers in hundreds of cities and towns. “He has been able to foster some great relationships between his staff and local public staff at a time when they were strained when he came in as commissioner.”

For instance, Carbone said, a couple of years ago, legislators passed a law to better protect diners with food allergies, an action that would have required local health inspectors to enforce regulations. Carbone said Auerbach forged a compromise that lightened the load on inspectors by placing some of the responsibility on restaurants to demonstrate they were following the regulations.


Kay Lazar can be reached at klazar@globe.com.