The Emmanuel Apostolic Church and the Catholic Action Center are suing the city of Lexington over the location of their homeless shelter on Winchester Road.
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.