The incident involved a 55-year-old woman he knew, allegedly grabbing the woman's butt in his apartment last October, authorities said.
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The woman reported the incident in July, and Frieden turned himself in to special victims in Brooklyn Friday morning.
He is charged with forcible touching, sex abuse, and harassment.
"This allegation does not reflect Dr. Frieden's public or private behavior, or his values over a lifetime of service to improve health around the world," a spokesman for Dr. Frieden said.
Frieden is also the former head of the Center for Disease Control and Prevention. He currently leads the $225 million Resolve to Save Lives initiative, housed at a nonprofit global health organization called Vital Strategies.
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Jose Castro, president and CEO of Vital Strategies, issued the following statement:
"In April of this year, Dr. Tom Frieden, who heads our Resolve to Save Lives Initiative, informed me that a non-work-related friend of his and his family of more than 30 years accused him of inappropriate physical contact. I have known and worked closely with Dr. Frieden for nearly 30 years and have seen first-hand that he has the highest ethical standards both personally and professionally. In all of my experiences with him, there have never been any concerns or reports of inappropriate conduct. Vital Strategies is committed to a workplace that is free of sexual harassment. As such, even though she is not an employee, earlier this month we conducted a thorough investigation by an external expert, which included an in-depth interview with every staff member on the Resolve to Save Lives team to determine whether there are any concerns about inappropriate behavior. This assessment determined there have been no incidents of workplace harassment. Vital Strategies greatly values the work Dr. Frieden does to advance public health and he has my full confidence."
Frieden was a CDC disease investigator in 1990 when he was assigned to New York City and worked on a large outbreak of drug-resistant tuberculosis. He stayed, taking a job heading the city's tuberculosis control.
In 1996, he began working in India with the World Health Organization on tuberculosis control.
New York Mayor Michael Bloomberg, elected in 2001, tapped Frieden to be the city's health commissioner.
Frieden became known for his aggressive measures to attack chronic diseases. In 2003, New York banned smoking in almost all workplaces, a precedent-setting move that inspired other cities to do the same. In 2006, it became the first U.S. city to ban restaurants from using artificial trans fats and required hundreds of eateries to post calorie counts on their menus.
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In 2009, President Barack Obama's administration picked Frieden to head the CDC. Frieden led U.S. public health efforts during a range of high-profile national and international health crises, including pandemic flu, Ebola and Zika.
Frieden was CDC director until January 2017, when he resigned as part of the turnover to President Donald Trump's administration.
In September 2017, Frieden announced he had moved back to New York City to head a $225 million initiative called Resolve to Save Live, housed at a nonprofit global health organization called Vital Strategies.
(The Associated Press contributed to this report)
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