The official, who was not authorized to speak ahead of the announcement and spoke on the condition of anonymity, says Poonam Alaigh will submit her resignation to the governor. No reason was immediately given.
Alaigh's department has been caught up in disputed policy decisions such as trying to implement a medical marijuana law and cutting funding for women's health clinics.
Democrats also have criticized Alaigh's decision to delay implementing a law requiring restaurants to display calorie counts on menus.
The 46-year-old Warren resident is an internist specializing in vascular disease. She was executive director of Horizon Blue Cross Blue Shield of New Jersey before joining the administration.