Instability of stratified multi-phase flow in a rotating platform becomes important because of a potential role in micro-mixing and micro-machines. Centrifugal actuation can play an important role in driving the flow and Coriolis force can enhance the mixing in a short span by destabilizing the flow. In this study, we focus on the impact of the Coriolis force on a rotating viscosity-stratified flow with a thin diffusive mixed layer between two fluid layers. Modal stability analysis is used to estimate the critical parameters, namely Rotation number, Reynolds number, and wave number, which are responsible to modulate the instability mechanism for different viscosity contrasts. Present study explores competing influences of rotational forces against the viscous and inertial forces. Correspondingly, rotational direction (clockwise/anticlockwise) shows a significant effect on the spatio-temporal instability mechanism and anticlockwise rotation promotes the instability. Usually, miscible viscosity stratified flow with respect to streamwise disturbance becomes more unstable for a thinner mixed layer. On the contrary, our numerical computation confirms a completely contrasting scenario, considering Coriolis force driven instability of a miscible system on account of spanwise disturbances. Possible physical mechanisms for the same are discussed in terms of base flow and energy fluctuation among perturbed and base flow. Comparison of two and three-dimensional instability is done to give a clear-cut idea about the linear instability of the flow system considered herein. Velocity and viscosity perturbation distributions display a critical bonding between the vortices near and away from mixed layer, which may be responsible for the variation of instability with respect to viscosity ratio and rotational direction.