He's referring to the ordinance that they can't run "at large" (meaning their pen needs to be fully enclosed). You can find the link to the code for Section 18-91 here.
You may be exempt from the code, however, if you clip their wings (being that they can't fly out through the top). However...
You can have them, so long as:
their housing is fully enclosed AND
their housing is 75' or more from the nearest residential or commercial building that you don't own AND
they don't put off an offensive odor AND
they don't create noise that's deemed a nuisance
I would suggest that you ask...