The president also said he was creating a Food Safety Working Group to coordinate food safety laws throughout government and advise him on how to update them. Many of these laws, essential to safeguarding the public from disease, haven't been touched since they were written in the time of President Theodore Roosevelt, he said.
Obama said the food safety system is too spread out, making it difficult to share information and solve problems.
He also blamed recent underfunding and understaffing at FDA that has left the agency unable to conduct annual inspections of more than a fraction of the 150,000 food processing plants and warehouses in the country.
"That is a hazard to public health. It is unacceptable. And it will change under the leadership of Dr. Margaret Hamburg," Obama pledged.
Hamburg, 53, is a well-known bioterrorism expert. She was an assistant health secretary under President Bill Clinton and helped lay the groundwork for the government's bioterrorism and flu pandemic preparations.
As New York City's top health official in the early 1990s, she created a program that cut high rates of drug-resistant tuberculosis.
She is the daughter of two doctors. Her mother was the first black woman to earn a medical degree from Yale University, and she credits her Jewish father for instilling in her a passion for public health.
Sharfstein, 39, is a pediatrician who has challenged the FDA on the safety of over-the-counter cold medicines for children. He also served as a health policy aide to Rep. Henry Waxman, D-Calif., who plays a leading role in overseeing the pharmaceutical industry.
Both are doctors and outsiders to the troubled agency who will face the daunting challenge of trying to turn it around.
Hamburg's appointment requires Senate confirmation; Sharfstein's does not.
Obama said while he doesn't believe government has the answer to every problem, there are certain things that only government can do such as "ensuring that the foods we eat and the medicines we take are safe and don't cause us harm."
"Protecting the safety of our food and drugs is one of the most fundamental responsibilities government has," he said.
Obama cited a string of breakdowns in assuring food safety in recent years from contaminated spinach in 2006 to salmonella in peppers and possibly tomatoes last year. This year, a massive salmonella outbreak in peanut products has sickened more than 600 people, is suspected of causing nine deaths and led to one of the largest product recalls in U.S. history.