The main contributor to spatio-temporal variability in the solar resource is clouds passing over photovoltaic (PV) modules. Cloud velocity is a principal input to many short-term forecast and variability models. In this paper spatio-temporal correlations of irradiance data are analyzed to estimate cloud motion. The analysis is performed using two spatially and temporally resolved simulated irradiance datasets generated from large eddy simulation. Cloud motion is estimated using two different methods; the cross-correlation method (CCM) applied to two or a few consecutive time steps and cross-spectral analysis (CSA) where the cloud speed and direction are estimated by cross-spectral analysis of a longer time series. CSA is modified to estimate the cloud motion direction as the case with least variation for all the velocities in the cloud motion direction. To ensure reliable cloud motion estimation, quality control (QC) is added to the CSA and CCM analyses. The results show 33% (52) and 21% (6) improvement in the cloud motion speed (direction) estimation using the modified CSA and CCM over the original methods (without QC), respectively. In general, CCM results are accurate for all the different cloud cover fractions with average relative mean bias error (rMBE) of cloud speed and mean absolute error of cloud direction equal to 3% and 3, respectively. For low cloud cover fractions, CSA estimates the cloud motion speed and direction with rMBE and mean absolute error equal to 10% and 11, respectively. However, for high cloud cover fractions and unsteady cloud speed, CSA results are not reliable for 3-4 h time series; however, splitting the whole time series into shorter time intervals reduces the rMBE and mean absolute error to 15% and 16 respectively.