This paper proposes a control method that can balance the input current of the three phase, three wire, Boost rectifier under unbalanced input voltage condition. The control objective is to operate the rectifier in the high power factor mode under normal operating condition but to give overriding priority to the current balance function in case of unbalance in the input voltages. The inner loop implements resistor emulator type input current shaping strategy. The outer control loop performs magnitude scaling and phase shifting operations on current of one of the axis to make it balanced with respect to the current on the other axis. The coefficients of scaling and shifting functions are determined by two closed loop PI controllers. The control method is input voltage sensorless. In implementation Texas Instrument's DSP TMS320F240F is used as the digital controller.