High penetration photovoltaic power generation system (PVS) may cause negative impacts on the frequency control of electric power system. In the impact assessment of high penetration PVS on the system frequency, the proper preparation of time-series data of aggregated PVS power output in electric power system service area is essential. However, the available data points are limited compared to the huge installation points of widely dispersed PVS in a power system service area. Therefore, this study proposes a modelling of aggregated PVS power output based on a low-pass filter (LPF) which is capable to take into account a smoothing effect of power output fluctuation around individual observation point. Then, the proposed model is applied to estimate the spatial average irradiance in the central region (called the Chubu region) in Japan by using the irradiance data observed at 61 points. The reduction in the short-cycle fluctuation is evaluated in comparison to the time-series data calculated by the simple average of 61 points data. Finally, the usefulness of proposed model is discussed in the situation that the aggregated PVS power output in electric power system service area must be curtailed due to the surplus power supply in the electric power system.