WASHINGTON — Deep-fried catfish served with a side of hush puppies and coleslaw has been a regional specialty for years and a cash crop for states in the Deep South. Now, catfish is at the heart of a dispute as the House and Senate prepare to work out their differences on a new five-year farm bill. The current bill expires on Sept. 30.

At issue is a little-known provision in the 2008 bill that established an office within the Agriculture Department to inspect catfish. But those inspection programs also exist at the Food and Drug Administration and the National Oceanic and Atmospheric Administration at the Commerce Department.

The Agriculture Department has traditionally inspected meat and poultry while the F.D.A. has inspected all other foods, including seafood.

Since 2009 the Agriculture Department said that it has spent $20 million to set up the catfish inspection office, which has a staff of four. The department said that it expects to spend about $14 million a year to run it. The F.D.A. spends about $700,000 a year on its existing office.