Al Armendariz had come under fire after comments he made in 2010 surfaced in which he had compared his enforcement strategy to the way ancient Roman conquerors would use terror, in the form of crucifixions, to keep order, The Hill reported Monday.
A number of Republican lawmakers had called for the resignation of Armendariz, EPA's Region 6 administrator whose responsibility included oil-and-gas producing states such as Texas and Louisiana, despite his apology for the remarks.
EPA Administrator Lisa P. Jackson announced Armendariz's departure in a statement.
"Over the weekend Dr. Armendariz offered his resignation, which I accepted. I respect the difficult decision he made and his wish to avoid distracting from the important work of the agency. We are all grateful for Dr. Armendariz's service to EPA and to our nation," she said.
In his resignation letter to Jackson, Armendariz said his 2010 comments were not an accurate characterization of his approach to his responsibilities.
"As I have expressed publicly, and to you directly, I regret comments I made several years ago that do not in any way reflect my work as regional administrator. As importantly, they do not represent the work you have overseen as EPA administrator," he wrote.