The city is revoking the building permit, saying the building was to be used as a church only, and not as a homeless shelter.
Officials with the Community Inn say they have been working closely with the city since January of 2011, gaining all the necessary permits to set up a homeless shelter. They say not once did the city have any issue with their plans.
The property is zoned B-4 for wholesale and warehouse use. Churches are allowed in the area as a conditional use.
The building houses homeless men and women seven nights a week. Neighbors and area businesses have complained about the number of homeless people in the area.
ABC 36 News contacted the city for comment. A spokeswoman said there would be no comment due to the pending litigation.