Margaret Hamburg told employees of the FDA in an email that the agency's chief scientist, Stephen Ostroff, will serve as acting commissioner.
She is among the longest-serving commissioners to head the agency and helped oversee the creation of a new food safety system, reforms in how drugs are reviewed and new tobacco regulations.
President Barack Obama named Hamburg to the post in 2009, following a series of high-profile safety problems at the agency ranging from contaminated drugs to salmonella-tainted peppers to peanut butter that required one of the largest food recalls in US history.