If convicted, Lyon could face up to 15 years in prison.
Nick Lyon, director of Michigan Health and Human Services, "failed in his responsibilities to protect the health and safety of the citizens of Flint", state AG Bill Schuette said at a press conference Wednesday.
The state's chief medical officer, Dr. Eden Wells, was charged Wednesday with obstruction of justice and lying to an investigator.
Snyder went on to say Lyon is a strong leader who remains completely committed to Flint's recovery. Legionnaires' is a type of bacterial pneumonia that experts have linked to contaminated water.
In May, Schuette dropped a misdemeanor charge against a Flint official who cooperated after pleading no contest to willful neglect of duty.
According to Snyder, Lyon and Wells, "like every other person who has been charged with a crime by Bill Schuette, are presumed innocent unless and until proven guilty".
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.
The Michigan Department of Health and Human Services had no comment when asked about the employment status of Lyon and Wells, who are both still listed on the department website under executive bios. He also charges Earley, Ambrose and two Flint city employees with felony counts of false pretenses and conspiracy to commit false pretenses in the issuance of bonds to pay for a portion of the water project that led to the crisis.
She is also alleged to have lied to law enforcement about when she knew about the outbreak, a two-year charge.
Lead in water supplies can cause profound and permanent health problems, particularly in children whose brains and nervous systems are still developing.
All defendants charged with involuntary manslaughter are charged in relation to the death of Robert Skidmore, 85, of Mt. Morris, Michigan.