President Donald Trump says Environmental Protection Agency administrator Scott Pruitt resigned on his own accord and there was 'no final straw".
Trump told reporters on Air Force One on Thursday en route to Montana that Pruitt "did an outstanding job".
Pruitt's management of the agency has prompted a series of investigations.
"He came to me and said I have such great confidence in the administration I don't want to be a distraction," Trump told reporters.
Trump said they had been talking about Pruitt's exit for a "little while," adding "He'll go and do great things".
Trump tweeted earlier on Thursday that Pruitt had resigned. He will be replaced by acting administrator Andrew Wheeler.
Pruitt had become a constant source of embarrassment to a president who had entered Washington promising to "Drain the Swamp".
Pruitt has faced an array of ethical questions about his travel spending, security costs, dealings with industry lobbyists and misuse of government resources.
He had denied wrongdoing in the face of multiple congressional and oversight inquiries.
Despite the scandals, Trump has been approving of Pruitt's efforts to reduce regulations that the administration says curb business growth. Trump writes on Twitter, "Within the Agency Scott has done an outstanding job."
Activists have argued those cuts have endangered the environment.
Trump tweets that Deputy Administrator Andrew Wheeler will assume the acting administrator position Monday.