Inspector General Glenn Cunha will take over the investigation into the operations of the Jamaica Plain drug lab, where former state chemist Annie Dookhan allegedly tainted evidence in thousands of cases, Governor Deval Patrick said today.

In a statement, Patrick said Cunha will now take over the sweeping inquiry into the closed Department of Public Health lab where Dookhan worked from 2003 to 2012. Cunha is replacing Attorney General Martha Coakley who will continue to pursue a criminal investigation into Dookhan.

Coakley’s position in seeking to prosecute Dookhan, along with her office’s prior advocacy of the quality of the science at the lab in courthouses earlier this year, led the Massachusetts Bar Association and the American Civil Liberties Union of Massachusetts to seek her ouster from the lab investigation.

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“Inspector General Cunha brings the necessary independence and experience to the task and enjoys the support of both prosecutors and the defense bar,” Patrick said in announcing the changeover to Cunha. “I look forward to his findings.”

Cunha was named inspector general in July and previously had been an assistant attorney general who led investigations into the Chelsea Housing Authority, human trafficking, and other criminal matters.

“The integrity and credibility of the criminal justice system require a comprehensive and thorough review of the drug lab,” Cunha said in a statement. “My office is prepared to conduct such a review and to that end, I have already begun to assemble an experienced team to examine the lab’s operations, paying particular attention to its policies and procedures.”

Cunha plans to hire independent forensic experts “to determine whether potential failures at the drug lab impact cases beyond those handled directly by Dookhan,’’ according to Patrick’s statement. Cunha’s work will proceed alongside David Meier’s “boiler room’’ operation, in which the Boston attorney is trying to match potentially tainted drug samples to criminal defendants. So far, Meier has connected Dookhan-tested drug samples to 1,900 defendants.

Martin Healy, chief legal counsel to the Massachusetts Bar Association, said in the same statement that the Cunha appointment should mean an “independent investigation of the drug lab.’’

Coakley, through aides, welcomed the opportunity to step aside from what promises to be a time-consuming, costly inquiry that she believes must help restore public confidence in the state’s criminal justice system.

Dookhan has pleaded not guilty to two counts of obstruction of justice and a charge of inflating her academic resume. She has pleaded not guilty and is free on $10,000 cash bail.

Dookhan allegedly confessed to State Police assigned to Coakley’s office earlier this year that she manipulated the weights of some drug samples, tampered with samples to turn a negative result into a positive, and violated lab protocols aimed at protecting the integrity of testing.

Credible scientific testing of substances seized in drug arrests is crucial to such cases. Otherwise, defendants could argue that the substances found on them were not really illegal drugs.