Induced EMF in a transformer
If you force a voltage in the primary (voltage source connected to the primary), then this is the voltage you'll have in the primary ("nature" can't change that). Then the magnetic flux will be such that you get this voltage in the primary (so that the Faraday law holds true). And finally the current will be such that you get this magnetic flux. 

This is the variables causal relationship in your configuration (voltage source attached to the primary):

Voltage(t) -> Flux(t) -> Current(t)