The New York police department said Thomas Frieden was arrested on Friday morning in Brooklyn. It said she reported it in July.
It is unclear if he has an attorney.
He is now in NYPD custody and is expected to head to Brooklyn Criminal Court for arraignment.
In his former job, he led CDC work that is credited with helping to end the Ebola epidemic. He turned himself in to the NYPD on Friday and faces two misdemeanor charges of forcible touching and sexual abuse, as well as harassment, a violation, reports the Daily News.
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In 2015, Hunter told his wife he wanted to buy a pair of "Hawaii shorts" but had run out of money, the indictment said. Gregory Vega, Hunter's lawyer, said: "The congressman has faced more hard battles than this in Iraq and Afghanistan".
An order of protection was issued, and Frieden is to have no contact with the alleged victim, according to the district attorney's office.
"I have known and worked closely with Dr. Frieden for almost 30 years and have seen first-hand that he has the highest ethical standards both personally and professionally", Castro said.
In the '90s, he led a program to control tuberculosis in a NY, lowering incidences whereby people were resistant to multiple drugs.
He added that Vital Strategies had conducted an investigation in which every staff member of his team was interviewed.
Its president and CEO, Jose Castro, told CNN that the groping accusation came from a friend who knew him and his family for more than 30 years. That led to work with the World Health Organization's TB program in India. Frieden surrendered his passport and is next due in court on October 11, prosecutors said. In 2006, it became the first US city to ban restaurants from using artificial trans fats and required hundreds of eateries to post calorie counts on their menus. He was appointed to head the CDC by former President Barack Obama in 2009.