  We examine the soft supersymmetry breaking parameters induced by the
Scherk-Schwarz (SS) boundary condition in 5-dimensional orbifold field theory
in which the quark and lepton zero modes are quasi-localized at the orbifold
fixed points to generate the hierarchical Yukawa couplings. In such theories,
the radion corresponds to a flavon to generate the flavor hierarchy and at the
same time plays the role of the messenger of supersymmetry breaking. As a
consequence, the resulting soft scalar masses and trilinear $A$-parameters of
matter zero modes at the compactification scale are highly flavor-dependent,
thereby can lead to dangerous flavor violations at low energy scales. We
analyze in detail the low energy flavor violations in SS-dominated
supersymmetry breaking scenario under the assumption that the compactification
scale is close to the grand unification scale and the 4-dimensional effective
theory below the compactification scale is given by the minimal supersymmetric
standard model. Our analysis can be applied to any supersymmetry breaking
mechanism giving a sizable $F$-component of the radion superfield, e.g. the
hidden gaugino condensation model.
