The magnetotelluric (MT) method has been among the favorite supporting tools for seismic imaging of sub-salt and sub-basalt targets. In this paper we present an example from Kachchh, India (where basaltic rocks overlie Mesozoic sedimentary rocks), and discuss the feasibility of using MT method as an exploration tool in this geological setting. Our results highlight the difference in magnetotelluric response caused by the thin intra-basalt layering. The key issue addressed in this paper is what MT can and cannot provide in such geological settings. First, we compute apparent resistivity and phase response curves using representative resistivity-depth models and borehole data from the study area. Later, we compare these results to assess the plausibility of using MT to image the sub-volcanic sediments at Kachchh. Finally, we substantiate our discussion through one-dimensional inversion of the field observed MT data from this region that exhibits poor sensitivity of MT for thin basalt layers.