How to provide an overload protection to an electric motor when the amperage reading in each phase is different?
The amperage draw should not be different, or at least should be minimal. For example if the motor is a three phase 5HP 575V motor the nameplate amps will be roughly 5A. It will vary slightly from motor to motor. All 3 phases should draw within 3% or so of each other: 4.8, 4.9, 4.75. Overload protection and fusing are not the same and BOTH should be used. Overload should be set at, or slightly above, the nameplate amps. The fuses should be 175% higher. Overload protects the motor, fuses protects the line.
Your amperage draw should have a minimal difference between the phases, not enough to require different overload protection. If there is significant difference you either have a motor problem or a supply issue. Start with the supply make sure the voltage is the same in all phases.