A controller reduction technique is presented for unstable systems via structurally balanced truncation (SBT) based on coprime factorization. Coprime factorization of the full order controller is utilized to preserve the characteristics of the closed loop system including the reduced order controller, in spite of unstable poles of the system. SBT is introduced as a substitute for balanced truncation to reduce the norm error of closed-loop transfer function. Numerical study of balanced truncation and SBT with coprime factorization illustrates the feasibility of the proposed technique for a flexible beam example with poles at the origin.