By Suzannah Gonzales and Chris Kenning

(Reuters) – Michigan sued the city of Flint on Wednesday in federal court over its failure to approve a long-term drinking water source for residents.

Flint switched its water supply in 2014, sparking a crisis that was linked to an outbreak of Legionnaires’ disease and at least 12 deaths, as well as exposure of residents to dangerously high lead levels. Since October 2015, the city has obtained its water from the Great Lakes Water Authority.

But the Flint city council’s refusal this week to approve a long-term agreement with the supplier, negotiated by the city’s mayor, without proposing a reasonable alternative, will “cause an imminent and substantial endangerment to public health in Flint,” according to the lawsuit filed by the Michigan Department of Environmental Quality in U.S. District Court in Detroit.

The state is asking the court to bar Flint from changing water sources and adopt the long-term agreement.

“While disappointing that the state and federal government are now involved in making a decision we as city leaders should be making for Flint, I cannot say that I am surprised,” Flint Mayor Karen Weaver said in a statement. She added that her plan was best option.

Instead of approving the long-term agreement, the city council voted on Monday to extend until September its contract with the Great Lakes Water Authority, local media reports said.

City Council President Kerry Nelson told the Detroit News the state’s June 26 deadline was too rushed for council members, who needed more time to examine the deal.

Michigan Governor Rick Snyder and state officials on Wednesday called on the council to approve the mayor’s deal.

“The city is well on its way to a full recovery, and to hinder that progress now would be a major and costly setback for residents,” Snyder’s spokeswoman, Anna Heaton, said.

The crisis erupted in 2015 after tests found high amounts of lead in blood samples taken from children in the industrial city of about 100,000, whose population is predominantly black.

The city had started using the Flint River for water in 2014. Water to Flint from the Great Lakes Water Authority comes from Lake Huron.

The more corrosive river water caused lead to leach from pipes and into the drinking water. Lead levels in Flint’s drinking water have now fallen below levels considered dangerous by federal regulators.

Earlier this month, six current and former Michigan and Flint officials were criminally charged for their roles in the crisis.

(Reporting by Suzannah Gonzales and Chris Kenning in Chicago; Editing by G Crosse, Matthew Lewis and David Gregorio)