Where in relation to rest of the ducting is the water coming out, at the end of the line or somewhere close to the duct coming down from the fan?
Is there any water coming out anywhere else in that particular run of duct work?
Is this happening with all the engine room fans or just one fan in particular?
Are there any kind of old unused heating or cooling coil, fire suppression spray nozzles or spray nozzles used for humidity control in duct work somewhere that may be leaking water into the air stream?
Have there been any checks for leaking pipes above the duct that would cause water to run around or along the outside of the duct?
Have there been any checks for holes in either the deck head directly above the fan or air intake, in any drain scuppers from the upper deck that may pass close to the fan intake or where the duct work passes through an exposed area of the deck? On one ship I was on we had similar problems, one turned out to be a leaking deck scupper drain and the other was holes in the duct right under the fan where it passed through the deck. After the rust, scale, cargo and other crap on the deck that built up around the duct was removed it was found that the duct was almost completely rotted away.
Troubleshooting 101 "Don't over think it - K.I.S.S. it"