Nick Lyon is accused of failing to alert the public about an outbreak of Legionnaires' disease in the Flint area, which has been linked by some experts to poor water quality in 2014 and 2015. The state's chief medical officer, Dr. Eden Wells, was charged with obstruction of justice and lying to a police officer.
Lyon's failure to act resulted in the death of at least one person, 85-year-old Robert Skidmore, special agent Jeff Seipenko told a judge.
The charges were read in court by Seipenko, a member of the state attorney general's team. Lyon and Wells were not in court. A message seeking comment was left for Lyon's attorneys. Wells' lawyer was not immediately known.
Flint began using water from the Flint River in 2014 but didn't treat it to reduce corrosion. Lead from old plumbing leached into the water system.
Some experts also have linked the water to Legionnaires' disease, a type of pneumonia caused by bacteria that thrive in warm water and infect the lungs. People can get sick if they inhale mist or vapor, typically from cooling systems.
There were nearly 100 cases in the Flint area, including 12 deaths, in 2014 and 2015.
Lyon was personally briefed in January 2015 but "took no action to alert the public of a deadly" outbreak until nearly a year later, Seipenko said.
Lyon has admitted that he was aware of Legionnaires' for months but wanted to wait until investigators in the Health and Human Services Department finished their own probe.
He told state lawmakers that experts likely wanted to "solve the problem" before they raised it with senior officials in the Snyder administration. The investigation, he said, "wasn't one that was easily solved."