The Michigan Supreme Court said Tuesday that indictments against former top state officials over the Flint water crisis had been issued improperly, upending some of the highest-profile prosecutions in recent state history and leaving residents whose tap water turned toxic without any accountability in criminal court.

In bringing charges last year against Michigan officials, including former Gov. Rick Snyder, prosecutors said they had failed to protect the safety and health of Flint residents, who were sickened by increased levels of lead and by Legionnaires’ disease after the city’s water supply was switched to the Flint River in April 2014.

But prosecutors appointed by Attorney General Dana Nessel, a Democrat, relied on a one-man grand jury to issue indictments against Mr. Snyder, a Republican, and eight others, including the former state health director and the state’s former chief medical officer. The Supreme Court said Tuesday that single-person grand juries could not be used in that way.

Three defendants, not including Mr. Snyder, had challenged the use of the one-man grand jury, but the court’s decision also appeared likely to upset the prosecutions of the other defendants. An official in Ms. Nessel’s office said prosecutors were reviewing the decision. It was not clear whether they intended to pursue new charges.

At least nine people died of Legionnaires’ in the Flint region from June 2014 through October 2015. The water crisis, which resulted in elevated lead levels among thousands of people in Flint, has left countless families distrustful of the water supply, even as city officials insist that it is now safe to drink.

The charges brought by Ms. Nessel’s team were a second attempt at prosecuting officials for what had happened in Flint. Before Ms. Nessel took office, her Republican predecessor helped oversee cases against 15 state and local officials for crimes as serious as involuntary manslaughter. But Ms. Nessel’s team had those cases dismissed in 2019 before filing new charges against several of the same officials.