This paper proposes an implementation method of a workspace observer (WOB) considering a fluctuation of an equivalent mass matrix. WOB is one of useful methods to achieve robust control systems. The stability and transient response of WOB is influenced from a modeling error of a nominal plant model. For a high performance of WOB, a precise modeling of a nominal plant model should be used. From this viewpoint, this paper modifies a nominal plant model in real time due to an estimation of an equivalent mass matrix. Here, a nominal plant model includes off-diagonal elements. An equivalent mass matrix is fluctuated due to a manipulator motion. This fluctuation is influenced to a control performance of WOB. Therefore, this fluctuation is compensated in this paper. In addition, a decoupling in an acceleration dimension is actualized, even if a nominal plant model includes off-diagonal elements. The validity of the proposed method was confirmed by simulation results.