The FNOA is located in the Naval Armory, which houses the ROTC divisions, but Phase II of the Master Plan involves demolishing the structure to build the new science complex.
But FNOA members are fighting to keep their 60-year-old building on the corner of South Columbia Street and South Road.
The officers are requesting a nomination from the N.C. State Historic Preservation Office to be listed on the National Register of Historic Places -- a move that would protect the building from being torn down.
But if the ROTC building is saved, that part of Phase II "can't be done," said Jonathan Howes, director of the Master Plan. "It would seriously change the kind of science complex that has been designed."
Phase II of the science complex project involves building a new multipurpose building that will include a parking deck, office research space and a science library in the ROTC building's location.
Phase II is not scheduled to begin until 2005. Officials will begin by clearing out Venable Hall and the ROTC building before eventually knocking them down.
The UNC Naval ROTC Alumni Association investigated the situation and determined that petitioning the University likely would not be effective.
"We've pretty much been told that there's no way the University won't tear it down, so we're trying to go above them," said FNOA President Mel Ahle.
The FNOA now is trying to save the building with the help of the national register.