There were 12 deaths and 79 other people sickened by Legionnaires' disease in 2014-15, which some experts have linked to the contaminated water after the city switched to Flint River water in April 2014.
Involuntary manslaughter is punishable by up to 15-years in prison and a possible $7500 fine.
The highest-ranking official in Michigan's health department has been charged with involuntary manslaughter for botching the response to adopting lead-tainted water supply, the Associated Press reported.
"We don't have a check list as to who should be charged with a crime and who should not be".
The charges were read in court by Seipenko, a member of the state attorney general's team.
The manslaughter charges are all related to the death of Mt. Morris resident Robert Skidmore, who died in December 2015.
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The state's culpability is rooted in the fact that Flint was being run by state appointed emergency managers at the time of the water crisis.
#Michigan Attorney General Bill Schuette announced the charges on Wednesday morning.
Shekter Smith's lawyer, Brian Morley, said: "It's my understanding neither she nor the Department of Environmental Quality were responsible for legionella issues".
Chip Chamberlain and Larry Willey are representing Lyon and called the charges "baseless".
In a probable cause statement filed by prosecutors Wednesday, Lyon is accused of having received notice of the Legionnaires' outbreak at least a year before informing the public and the governor. "We were not successful", Schuette said.
Listen to the entire conversation with Michigan Attorney General Bill Schuette and Genesee County Prosecutor David Leyton above.
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"Director Lyon and Dr. Wells have been and continue to be instrumental in Flint's recovery", he said in a statement. The two researchers were subpoenaed to testify in Schuette's investigation of Flint's water crisis, Wayne State University spokesman Matthew Lockwood said.
The more corrosive river water caused lead to leach from pipes and into the drinking water. People can get sick if they inhale mist or vapor, typically from cooling systems.
The U.S. Centers for Disease Control and Prevention also found blood samples showed children under the age of 6 were almost 50 percent more likely to have elevated levels of lead in their blood when the city used the Flint River for drinking water instead of the Detroit water system. He was admitted to McClaren Flint hospital in June 2015 with symptoms consistent with pneumonia.
Lyon was personally briefed in January 2015 but "took no action to alert the public of a deadly" outbreak until almost a year later, special agent Jeff Seipenko told a judge as the charges were filed.
Lyon is also being charged with misconduct in office due to allegedly "instructing an official to discontinue an analysis that would help determine the cause of the outbreak".
Schuette said the investigation was peer reviewed by numerous current and former litigators, and he is confident there is enough evidence to establish probable cause.
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