In a letter to UK Prime Minister Rishi Sunak on Tuesday, Williamson said he was "stepping back" from his office because the investigation into his past conduct was "becoming a distraction" for the government.
"I have therefore decided to step back from government so that I can comply fully with the complaints process that is underway and clear my name of any wrongdoing," he wrote.
In a response, Sunak wrote that he accepted Williamson's resignation "with great sadness."
"I support your decision to step back and understand why you have taken it. I would like to thank you for your personal support and loyalty," he added. "I also want to express my gratitude for the work you have done for this government."
Sunak appointed Williamson last month to support the Chancellor of the Duchy of Lancaster after Sunak won out among Conservative Party candidates to replace Liz Truss, who had recently quit Downing Street.
However, it soon emerged that a fellow lawmaker had made a complaint against Williamson the day before, alleging he sent them abusive messages prior to the funeral of Queen Elizabeth II in September. Williamson has apologized for the comments.
Then over the weekend, new accusations emerged of more abusive behavior by Williamson, including that while serving as the UK's defense secretary, he told a civil servant to "slit your throat" and another to "jump out of a window." Williamson has denied the "characterization" of the claims.