Hundreds of tons of toxic lead in Notre Dame's spire and roof melted during the April fire, and exceptionally high levels of lead were later detected in the surrounding air that settled on streets and buildings in the surrounding area.
In its lawsuit, environmental protection group Robin des Bois accuses French authorities of "wrongful failure" and that officials deliberately endangered human life.
"In three months, we have accumulated enough evidence of the inertia of the public authorities to decide to take legal action," Jacky Bonnemains, president of Robin des Bois, told French media.
The group filed the lawsuit on July 26, one day a day after a nursery and a school near Notre-Dame were shut following tests which found high levels of lead in their shared playground, Sky News reported.
The lawsuit does not name specific individuals as defendants. Paris City Hall would not comment on Tuesday, according to the Associated Press.
Paris officials last week ordered a deep cleaning for neighborhood schools, and health authorities recommended blood tests for children and pregnant women who live near Notre Dame.
One of the tests -- which was conducted in a private school -- showed 698 micrograms of lead per square meter, 10 times higher than the 70 microgram level considered potentially dangerous, according to Sky News.
Children are especially vulnerable to health problems from lead poisoning and exposure, which can cause nerve and brain damage in severe cases.
Three French charities and the country's culture minister signed an agreement Monday ensuring transparency in how donations to rebuild the damaged cathedral are used. An estimated $946 million have poured in from both within France and other parts of the rest of the world.
The agreement specifies that donations will be used exclusively for preservation and restoration work at Notre Dame and training experts with needed skills, the Culture Ministry said.
The Associated Press contributed to this report.