Estimation of directional frequency transfer functions of a running ship is important to estimate their behaviours in realistic short crested irregular waves (such waves are called as directional spectrum waves) Of course, there are some theoretical calculation methods for such directional response functions, but it seems that there are not so many experimental results confirming such theoretical ones. For that purpose, square basins are needed. On the other hand, recently the authors developed a wave maker which can generate directional spectrum waves in a long towing tank, and many experiments of running ships were conducted in such waves. In those experiments, obtained results are one dimensional motion spectra and direct comparison with theoretical ones is impossible. So we tried to make inverse estimation of directional transfer functions of a running ship using both one dimensional response spectrum measured in such waves and measured two dimensional directional wave spectrum. Estimated results by present method on heave, pitch, roll and vertical acceleration response functions are reported here, but this method will be also applicable to other situations like motions of a running ship in actual seas by measuring its motions and incoming directional waves.