It suggests Protestants considering moving to the shared housing estate would be "bombed out, burnt out and shot".
The "No prods in Feldon" writing also threated a member of Clanmil Housing Association, the body developing the site.
Politicians have called it an attempt to create a sectarian ghetto in Newtownabbey, according to UTV.
The project, estimated at about £11.5 million, is due to be finished in October.
Thomas Hogg, Antrim Mayor and DUP Newtownabbey Councillor, said: "The painting of this sectarian and threatening graffiti is the latest in a series of intimidating acts close to the Felden shared-housing development.
"There is clearly a concerted campaign aimed at deterring any unionists or Protestants from applying for these new social homes which will be allocated shortly."
He added that: "Social housing ought to be allocated on the bases of demonstrable need alone and it is despicable that bully-boy tactics are being employed to dissuade those in need from availing of these homes.
"The new development is of a magnitude that far exceeds the social-housing need in the immediate areas, so for the development to be justifiable it must meet the need of the wider Newtownabbey area."
The Ulster Unionist Party also condemned the writing, saying it was trying to whip up tensions in the area.
Belfast Live also reported that Andy Allen from the party said: "Clearly in spite of fine words of a shared future, and the noble intention of creating an area of shared housing, there are elements within the nationalist and republican community who are not prepared to share the Felden Housing site with anyone from a Protestant or unionist community background."
The graffiti has since been painted over.