The Government Accountability Office has identified U.S. food safety efforts as a critically flawed federal program. Specifically the agency cited the splintered arrangement by having multiple agencies monitoring a piece of the pie.

However, this assessment is something of a repeat from a similar assessment made several years ago. As a matter of fact, in 2002 GAO issued a similar report criticizing the Food and Drug Adminiatration, USDA and other agencies for discrepancies in food inspection oversight. Truth is, there doesn't appear to be a logical pattern for which agency does what.
For example, USDA has jurisdiction over sausage pizzas, while FDA reviews cheese pizzas. USDA continually inspects slaughterhouses, while FDA inspections occur sporadically.

The GAO recommendation is that federal oversight of food safety "be approached system-wide."

Given various widespread food contamination challenges last year (the most significant in produce), the call for a single food agency is loud and clear, and gaining traction. You can bet it will get serious discussion this year in Congress. 

Among those surely to light a fire under this issue are Sen. Hillary Clinton [D.-N.Y.], Sen. Richard Durbin [D.-Ill.] and Representative Rosa DeLauro [D-Conn.] They support legislation that calls for a single food agency.

A government spokesperson reports that USDA and FDA are talking in an attempt to sort out discrepancies and responsbilities among the two agencies.

As for whether the current system is working: "Since 1998, the Centers for Disease Control reports a sustained decline in the rates of foodborne illness," says the spokesperson. "Illnesses from E. coli O157:H7 has declined 29 percent; a 32 percent decline from Listeria monocytogenes; and a 30 percent decline in illnesses from Campylobacter."