This paper proposes an estimation algorithm for the separate primary and secondary leakage inductances of a three phase $Y-Delta$ transformer using least squares method. The voltage equations from the primary and secondary windings are combined into a differential equation to estimate the separate primary and secondary leakage inductances in order to use the line current of the delta winding. Separate primary and secondary leakage inductances are obtained by applying least squares method to the differential equation. The performance of the proposed algorithm is validated under transient states, such as magnetic inrush and overexcitation, as well as in the steady state with various cut-off frequencies of low-pass filter. The proposed technique can accurately generate separate leakage inductances both in the steady and transient states.