In order to estimate the total power output fluctuation of a high-penetration photovoltaic power generation system by using data from a limited number of points, the smoothing effect around individual observation points should be taken into account. Based on the transfer hypothesis, this study proposes a low-pass filter (LPF) to estimate the spatial average irradiance fluctuation characteristics taking the smoothing effect around the observation point into account. First, by using the irradiance data observed at 18 points in the Nobi plain, we confirmed that the fluctuation characteristics of the spatial average irradiance can be estimated by using the characteristics of the single point irradiance when the radius of the equivalent circular area is smaller than 30 km. Then, by formulating the relation between the area size and the fluctuation cycle from which the random fluctuation factor begins to increase, we developed a LPF to take the smoothing effect around the observation point into account. Finally, we demonstrated that the spatial average fluctuation characteristics can be estimated successfully for various area sizes within a radius of 20 km by applying a dedicated LPF according to the area size. C⃝ 2014 Wiley Periodicals, Inc. Electron Comm Jpn, 97(11): 1-9, 2014; Published online in Wiley Online Library (wileyonlinelibrary.com).