The influence of diurnal vertical migrations of walleye pollock on acoustic survey was investigated. The experiments were conducted at Musashi-Tai and off Shakotan Peninsula in northern Japan Sea using a split beam type scientific echo-sounder SIMRAD EK500. Area backscattering coefficient (SA) and target strength (TS) of walleye pollock were measured in the daytime and in the nighttime. Results showed that the SA in the nighttime was three times higher than SA in the daytime in Musashi-Tai. Also the SA in the nighttime was 1.4 times higher than that in the daytime off Shakotan Peninsula. However, there were no significant differences of in situ TS of walleye pollock between day and night in both areas. Since the remarkable vertical migration of walleye pollock in bottom layer was observed in echograms, it is concluded that the diurnal changes of SA were caused by underestimation due to the hiding of the shoal of walleye pollock in acoustic deadzone near the bottom in the daytime.