Joseph Goffman, whose nomination was held up by senators opposed to U.S. climate policies, has overseen work on new standards for power plants and vehicles.
The lawsuit, filed by the Justice Department, seeks millions in unpaid environmental fines as Gov. Jim Justice begins his campaign for the U.S. Senate.
The West Virginia senator contends the administration is defying Congress in its rollout of the last year's climate law. Some fellow Democrats fear he's undermining the legislation he shaped.