Dr. Edward Ehlinger resigned Tuesday as Minnesota's commissioner of health in the wake of published reports and controversy over the state's mishandling of allegations of criminal abuse in senior care facilities.

Deputy Commissioner Dan Pollock will serve as acting commissioner of the Health Department until a permanent replacement is appointed by Gov. Mark Dayton.

"We are grateful to Commissioner Ehlinger for his many years of dedicated public service," Dayton said in a written statement Tuesday afternoon. "I wish him the very best in his future endeavors. And I pledge to the many dedicated employees at the Health Department our strong support in their efforts to improve the health and safety of all Minnesotans."

In an unusual move, Dayton also gave the Minnesota Department of Human Services (DHS) sweeping new powers over the agency responsible for investigating abuse and neglect in senior care homes. The much-larger Department of Human Services will have the authority to direct Health Department staff, make personnel decisions and implement changes to the agency's work and investigative process, according to a far-reaching agreement reached Tuesday between the two agencies.

The Department of Human Services, the state's largest agency, which oversees programs that serve an estimated 1 million Minnesotans, will also make staff available to help the Health Department redesign its system for investigating allegations of maltreatment.

Ehlinger's resignation comes five weeks after a five-part Star Tribune series that chronicled breakdowns in the agency's handling of elder abuse allegations. The series documented that hundreds of residents at senior care centers across Minnesota are beaten, sexually assaulted or robbed each year. Yet the vast majority of these incidents are never resolved, and the perpetrators go unpunished, in part because the Health Department lacks the staff and forensic expertise to investigate them.

Even when abuse allegations are investigated, the cases can drag on for months, undermining criminal prosecutions and making it difficult for families to make informed decisions about care for their loved ones.

In a written statement after Dayton's office announced the restructuring, Human Services Commissioner Emily Piper said one of the top priorities will be improving communication with families of abuse victims, who are often kept in the dark while investigations drag on indefinitely. The Star Tribune series highlighted how, even in cases of serious abuse involving physical or sexual assaults, families are often told that the state's investigations are confidential and that they are not entitled to even basic details.

"Reports of abuse and neglect at nursing homes and care facilities should be handled swiftly to protect the safety of vulnerable Minnesotans and bad actors must be held accountable and brought to justice," Piper said.

The shake-up reflects manifold challenges the state faces as it struggles to catch up with a severe backlog of unresolved abuse and neglect cases. The number of allegations received by the Health Department has swelled from about 4,000 in 2010 to more than 25,000 in 2016. While agency officials say they review each of these allegations, only 3 percent were investigated on site by state inspectors, state records show.

In interviews, former employees at the agency described an office so overwhelmed by backlogged cases that workers dumped dozens of maltreatment complaints into recycling bins without reading them, according to a Star Tribune report. Others said unread complaint forms piled up into stacks 2 feet high and went unexamined for months.

Sen. Jim Abeler, R-Anoka, chairman of the Senate Human Services Reform, Finance and Policy Committee, said the decision to give DHS decisionmaking authority was "a sign of desperation" by the Dayton administration.

"This is a cry for help," Abeler said. "It's an admission of how bad things have gotten that they're essentially turning over the Health Department to another agency."

Public health pioneer

Ehlinger came to the Health Department in 2011 as a respected advocate for public health after several years running the University of Minnesota student health service. In his six years as commissioner, the agency placed new emphasis on reducing racial and economic health disparities across Minnesota and rolled out innovative projects to improve public health through preventive care, diet, fitness and other wellness activities.

A pediatrician and internal-medicine specialist, Ehlinger helped lead the state's effort to combat outbreaks of measles and bird flu, and also led the state's response to the global threat of Ebola. Over his tenure, Ehlinger pioneered an effort to define health in the broadest terms — for example, calling public attention to how adverse childhood experiences, such as abuse and family dysfunction, affect the lifelong health and well-being of people across the state.

"He was very forward-thinking on public health," said Sen. Michelle Benson, R-Ham Lake, chairwoman of the Senate Health and Human Services Finance and Policy Committee. "We didn't necessarily agree about the direction of public health, but he brought the department to a place where that is its core function."

Rep. Paul Thissen, the Minneapolis DFLer, added: "He's done amazing work and I think he really should be commended for that. But we cannot stand for the kind of behavior that was described in the Star Tribune [stories]. We owe our seniors and their families more than that."

In addition to taking steps to improve abuse investigations, Dayton last month announced the formation of a new elder abuse work group, led by AARP Minnesota, that will explore ways to improve the health and safety of Minnesota seniors in nursing homes and assisted-living facilities. That work group will make recommendations ahead of the 2018 Legislature.

Reporters J. Patrick Coolican and Jessie Van Berkel contributed.