A method and system for dual energy CT image reconstruction are provided. In one aspect, a fast kVp switching x-ray source is used during an imaging scan to produce a low energy x-ray beam for L consecutive projection angles, and then to produce a high energy x-ray beam for H consecutive projection angles, wherein L is substantially less than H. Various methods are provided for estimating the resulting undersampled data in the low energy projection data set and the high energy projection data set. The missing low energy projection data may be estimated from the known high energy projection data using any one of several disclosed structural propagation embodiments.