Police say the employee was looking for his iPod Sunday night when found the shotgun under a soda machine.
The employee told his supervisor, who notified authorities.
A police report says that a more thorough search of the break room turned up a container of gun lubricant and "tools for disassembly."
An Atlanta police officer did a background check on the weapon but could not immediately determine who owned it.
Airport spokesman John Kennedy said he couldn't comment because it was an ongoing investigation.