Calcium cobaltites, especially Ca₃Co₄O₉ with a misfit layered structure, are promising thermoelectric materials due to their suitability for high temperature applications and low densities. The existence of low spin-state electronic configurations for both and species is one of the key parameter to explain the large thermopower values. Ruthenium oxide, with a layered structure, exhibits strong electron-electron correlation and the extended nature of their 4d electrons enhances orbital overlapping which is expected to influence the transport characteristics of CaCo_1-xRu_xO_y (CCR) samples, by affecting the spin state of the 3d Co ions. The effect on thermopower and electrical resistivity due to partial substitution of Co by Ru ions, up to 0.33 moles, from 300 to 600 K was investigated. A sharp decline in resistivity and in thermopower was observed until a transition ion ratio (TIR), (Ru/(Ru + Co)), of 0.5 is reached, beyond which both the properties became less sensitive to TIR. These variations in the transport properties are explained by the presence of 4d Ru in close proximity to the Co, which could influence the spin and oxidation state of Co ions. The Co rich and Ru rich samples exhibit very distinct microstructures and phase assemblages.