Walter Shaub was appointed in 2013 to a five-year term as director of the Office of Government Ethics (OGE). He told Trump of his decision in a resignation letter.
Shaub will join the Campaign Legal Center, a non-profit group of election law experts, as its senior director of ethics.
In a parting statement yesterday, Shaub signaled there were mounting problems with reining in an administration that has faced many ethics complaints, and a White House occupant who proclaimed in January that he cannot have any conflicts of interest because he is president.
While he did not offer direct criticism in his letter to Trump, Shaub did say it had been a privilege to work with colleagues who protect the principle of placing "loyalty to the Constitution, the laws, and ethical principles above private gain."
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The White House said it accepted the resignation and that Trump will nominate a successor "in short order."
Even before Trump's inauguration, Shaub took issue with the billionaire president-elect about whether Trump appropriately divested from his global property empire.
Instead he ceded business control to his two adult sons -- a move that earned an OGE rebuke.
"It doesn't meet the standards that the best of his nominees are meeting and that every president in the last four decades has met," Shaub said at the time.
Trump's trust is "not even halfway blind," Shaub added. "His sons are still running the businesses, and, of course, he knows what he owns."
In February, Shaub urged the White House to investigate Trump aide Kellyanne Conway for plugging the fashion brand of the president's daughter Ivanka Trump during a TV interview, saying she should face "disciplinary" action for breaching standards of conduct.
The OGE has no investigative authority or power to enforce law. But the White House backed down and announced in May that the waivers would be publicly disclosed.
Top Senate Democrat Chuck Schumer hailed Shaub's service, and said his successor "must demonstrate that they are committed to... Ensuring administration officials are not using their positions for personal gain.