We study Fayet-Iliopoulos (FI) terms of 5-dimensional supersymmetric $U(1)$ gauge theory compactified on $S^1/Z_2$. In this model, loop diagrams including matter hypermultiplets and brane chiral multiplets induce FI-terms localized at the fixed points. Localized FI-terms lead instabilities of bulk modes. The form of the induced FI-terms strictly depends on wave function profiles of matter multiplets. It is a non-trivial question whether the vacuum of 1-loop corrected potential is stable under radiative corrections. We investigate this issue and it is found that the stable configuration is obtained when the bulk zero modes shield the brane charge completely.