A low-cost, small, lightweight hyperspectral sensor system that can be loaded onto small unmanned autonomous vehicle (UAV) platforms has been developed for the acquisition of aerial hyperspectral data. Safe and easy observation is possible under unstable illumination conditions by using lightweight and autonomous cruising. The hyperspectral sensor system, equipped with a 256-band hyperspectral sensor covering a spectral range from 340-763 nm, a GPS and a data logger, is 400 g in total weight. The acquisition period for each sampling, 768 bytes, is 100 ms. The aerial hyperspectral data of rice paddies are collected under cloudy weather. The flight altitude from the ground is 10 m, and the cruising speed is 2 m/s. The high-accuracy estimation of the chlorophyll densities is confirmed, even under unstable illumination conditions, by frequent monitoring of the illumination level and the chlorophyll indices, based on the red-edge (RE) and near infrared (NIR) spectral ranges.