Mandernach insisted in June that she would not resign, even after repeated calls for her ouster and marathon legislative hearings criticizing her leadership.
But Tuesday afternoon Mandernach sent an e-mail to Health Department staffers, saying she'd notified Gov. Pawlenty that she will leave her position on Oct. 2. Her last day of work will be Sept. 20.
Mandernach could not be reached for comment, and the e-mail offered no explanation for her decision.
In a statement, Gov. Pawlenty praised Mandernach's work in several areas, including emergency preparedness and reducing health disparities. He did not name a replacement.
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DFL House Majority Leader Tony Sertich of Chisholm said he was happy to hear of Mandernach's departure.
"I believe it was the right decision because the department needs to be held accountable," he said. "Moving forward, the Pawlenty administration has to renew the trust in the Department of Health for all of the people in Minnesota, and this is a good first step."
Sertich was one of several lawmakers from the Iron Range who called for Mandernach to resign in June. The criticism erupted in the wake of news reports indicating she had delayed the release of information on the cancer deaths of nearly three dozen miners.
Health Department officials learned in March 2006 that 35 miners on the Iron Range had died from mesothelioma, a rare lung cancer. Previous deaths had raised questions about the link between the disease and mine work. But Mandernach didn't reveal the 35 new deaths for a year.
At the time, Gov. Pawlenty criticized Mandernach but said he would not fire her. Mandernach said the decision to withhold the information was hers alone and she repeatedly apologized for it in public forums, including at a legislative hearing in June.
"Science and public health needs don't seem to me to be the primary driver of actions by the Department of Health."
"The decision I made was wrong and I apologize for it. At the same time, I hope we can move in a positive direction and agree to study this issue so that we can finally resolve all of the lingering questions," she said.
But her handling of the data raised even more questions about how Mandernach managed the department.
Over the past few months, several Health Department staffers have told Minnesota Public Radio News that they could not speak to a reporter about Mandernach for fear of being reprimanded or losing their jobs.
One former staffer, Diane O'Connor, said in June that the commissioner and other executives in her office were not interested in the information or expertise from rank-and-file staffers. O'Connor said politics, not science, drove the department.
"Science and public health needs don't seem to me to be the primary driver of actions by the Department of Health," she said.
O'Connor also said she was reprimanded for attending an event, simply because state lawmakers were present. She said the department had a policy forbidding staffers from talking to the press or to members of the Legislature.
The focus will now be on who Gov. Pawlenty selects as the next commissioner. It is one of the most difficult jobs in state government. The health commissioner has to understand and explain complicated science, as well as navigate the politics of controversial subjects like abortion.
Pawlenty is opposed to legalized abortion, and said in 2003 that Mandernach's views on abortion played a role in her appointment.
Scott Fischbach, executive director of the anti-abortion group Minnesota Citizens Concerned for Life, said he's disappointed to learn of Mandernach's resignation. He hopes Pawlenty will name a commissioner who shares Mandernach's views.
"Somebody who was very fair and open in dealing with abortion, infanticide and euthanasia that we focus on," he said. "So we would expect that the governor appoint somebody in the same mode as Diane Mandernach because she did such a good job."
Mandernach has been criticized for the way she handled one of the MCCL's highest legislative accomplishments in the past decade -- a law requiring women to wait 24 hours before getting an abortion.
Public health officials and the medical community said in 2004 it was wrong to suggest on a department Web site that abortion increased a woman's risk of breast cancer, since the information was not based on the latest, peer-reviewed science.
Sen. John Marty, DFL-Roseville, started calling for Mandernach's resignation then. He said he would prefer to see Pawlenty pick someone who is open, honest and puts science first.
"We don't need a rocket scientist for this," Marty said. "We just need someone who is going to play fair and work hard for the public's interest."
Mandernach said in her e-mail to staffers that she plans to spend more time with her family before deciding on any future career plans.