Winds up to 66 miles per hour sent the BAE Systems guard shack into the water, AL.com reported.
Steve Huffman, spokesman for the Mobile Fire-Rescue Department, said an unidentified 35-year-old man pulled from the water was treated for mild hypothermia and taken to a hospital.
The second unidentified man had not been found.
The guard shack was on a dry dock near where the Carnival Triumph was docked for repairs. The strong winds tore the cruise ship from its mooring lines, sending it into other vessels and docks.