Dianna Lightfoot had been under scrutiny by critics for partisan comments on her Twitter and Facebook social media accounts.
Screen shots of comments sent to the media included a reference to Hillary Clinton as part of Obama's "butch bunch" and multiple expressions of her opposition to health care reform as a "bully mandate."
In one Twitter post, she apparently suggests ultrasonic waves caused the massive earthquake in Japan.
"don't ultrasonic waves have potential to create earthquakes, look who's next door," she writes in an apparent reference to China or North Korea.
In a Facebook post, Lightfoot credits President Bush for killing Osama bin Laden. In another, she applauds Kansas Governor Sam Brownback for signing a bill banning Muslim Shariah law.
In another Facebook post, Lightfoot links to an ABC11.com article on the North Carolina amendment banning gay marriage expressing her support for it.
Lightfoot's Twitter account "chinalight44" had been taken down as of Thursday.
In a statement to ABC11, DHHS Spokeswoman Julie Henry said Lightfoot had decided to step down because she didn't want to become a distraction to the department.