The shutdown of a Massachusetts drug lab could be a boon to defense lawyers and their clients whose convictions were based on the actions of a chemist accused of mishandling drug evidence.

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The shutdown of a Massachusetts drug lab could be a boon to defense lawyers and their clients whose convictions were based on the actions of a chemist accused of mishandling drug evidence.

The Hinton State Laboratory Institute in Boston was closed Thursday after state police say they discovered that the chemist failed to follow testing protocols, potentially exposing thousands of drug convictions to legal challenges.

The lab was involved in certifying drug evidence in cases submitted by local police from around the state, including Boston. Massachusetts Attorney General Martha Coakley is conducting a criminal investigation. Police have not named the chemist, and she has not been charged.

Defense lawyers were swift to react. Several said they plan to challenge the results of any drug certification performed by the chemist.

“It’s going to throw the system into some confusion for a while,” said John LaChance, a Framingham defense attorney. “If a case has been closed, they (prosecutors) are going to have to go back and look through those cases to see if protocols were followed, and if the protocols weren’t followed, they should have to notify counsel or the defendants themselves so they can file a motion for a new trial or a motion to vacate a guilty plea.”

Larry Tipton, who heads the Norfolk Superior Court office of the Committee for Public Counsel Services, said problems can occur with a crime lab that is not independent and “is run basically by law enforcement.”

“There’s just not sufficient safeguards, and there’s an inherent bias that exists because the people that are conducting the tests are working for, basically, law enforcement, and to a lesser extent, the prosecution.”

In recent years, testing protocol violations have led to lab closures and case dismissals around the nation.

Hundreds of drug cases were thrown out in San Francisco after a lab technician was accused of skimming cocaine from evidence. In Nassau County, N.Y., officials last year closed their lab amid concerns over inaccuracies with testing in drug and drunken driving cases, which led to an extensive review. And a crime lab in Detroit was shut down in 2008 after outside auditors uncovered serious errors in the way evidence was handled.

Gov. Deval Patrick called the chemist’s alleged violations “deeply troubling,” and said he instructed the Massachusetts State Police to close Hinton lab.

“No breach this serious can or will be tolerated,” Patrick said in a statement.

State police spokesman David Procopio said district attorneys and public defenders were notified Thursday about the alleged violations. He said the next step is for state police to identify which cases the chemist worked on and then to give that information to prosecutors so they can take the appropriate action.

Procopio said the chemist performed thousands of tests since she began working at the lab in 2003, but it is unclear how many drug cases she may have mishandled. The chemist resigned in March during an internal investigation by the Massachusetts Public Health Department, which ran the lab at the time.

“This is more than just allegations of sloppiness and cutting corners,” Procopio said. “The allegations include malfeasance, deliberate mishandling … We are concerned that in some of the cases, there’s a likelihood that justice was not served, that a defendant did not get a fair trial and that it’s possible that people may be incarcerated unjustly.”

Ten other chemists who worked at the lab were placed on administrative leave and will eventually be sent to work at another of the nine state police labs. Procopio said those chemists are not suspected of any wrongdoing.

Tipton said public defenders in his office began hearing about problems at the lab months ago. He said one public defender in his office received a letter in February from an assistant district attorney who said a chemist was being investigated for a “possible breach of protocol” with respect to some drug samples. The prosecutor identified the chemist as Annie Dookhan.

Dookhan could not immediately be reached for comment. She appeared to have a nonpublished telephone number.

WHDH television station in Boston reported that the woman’s husband said in a statement that “my wife maintains her innocence … more than one person was involved in botching a drug procedure. We believe it’s co-workers who are trying to create a scapegoat.” The station did not name the husband.

Chemists at the lab performed drug certifications for local police departments, who then give the results to prosecutors. For example, if someone is arrested for having a white powdery substance, a chemist tests the substance, then certifies whether it is cocaine and certifies its quantity so that prosecutors can use it as evidence in a criminal case.

In June, state police were informed about inconsistencies in the chemist’s work at the lab. State police took over operation of the lab in July as part of a budgetary directive, and began their own audit. Within the last few days, state police realized the “large scope” of the inconsistencies and decided to close the lab, Procopio said.

Brad Puffer, a spokesman for Coakley, said state police informed the attorney general’s office in July about allegations regarding the possible improper handling of drug evidence. Puffer said Coakley’s office has interviewed dozens of people and developed evidence that certain required procedures were not followed.

Associated Press writer Bridget Murphy contributed to this report.