Lightweight unmanned autonomous vehicles (UAVs) are becoming practical platforms for aerial data acquisition. We developed a low-cost, small, lightweight hyperspectral sensor system that can be loaded onto small UAV platforms. The hyperspectral sensor system of the total weight 400 g is equipped with a 256-band hyperspectral sensor covering a spectral range from 340-763 nm, a GPS and a data logger. The acquisition period for each sampling is 200 ms. The aerial hyperspectral data of rice paddies acquired from an altitude of 10 m above ground level are collected under cloudy weather. The high-accuracy estimation of the chlorophyll densities is confirmed by the chlorophyll indices based on the red-edge (RE) and near infrared (NIR) spectral ranges, even under unstable illumination conditions.