In this work we propose an approach to solving a source estimation problem based on representation of carbon dioxide surface emissions as a linear combination of a finite number of pre-computed empirical orthogonal functions (EOFs). We used National Institute for Environmental Studies (NIES) transport model for computing response functions and Kalman filter for estimating carbon dioxide emissions. Our approach produces results similar to these of other models participating in the TransCom3 experiment. <br></br> Using the EOFs we can estimate surface fluxes at higher spatial resolution, while keeping the dimensionality of the problem comparable with that in the regions approach. This also allows us to avoid potentially artificial sharp gradients in the fluxes in between pre-defined regions. EOF results generally match observations more closely given the same error structure as the traditional method. <br></br> Additionally, the proposed approach does not require additional effort of defining independent self-contained emission regions.