Airport police were evacuating the airport's Terminal 1 as they looked for the person, the dpa news agency reported.
No further details on how the person might have made it past security checks were available, and neither the airport media office nor airport police would elaborate.
The local Stadt-Anzeiger newspaper reported that the airport police sent out the security alarm at 11:30 AM local time on suspicion that a person had entered the secure area of the airport through an exit.
In March, Cologne-Bonn's Terminal 2 was temporarily shut down after a 23-year-old woman skirted the security controls.
Police were able to find her and determined that she had simply been in a rush to catch her plane, but that incident meant delays for about 1,000 travelers.