Two preparation techniques (ion-exchange with Ru3(NH3)3+6 and vapor impregnation by Ru3(CO)12) have been employed to prepare ruthenium metal clusters encaged in the pores of Y zeolite and their catalytic behaviors for CO hydrogenation were compared. The reaction was examined with a differential reactor operating at atmospheric pressure, a fixed temperature of 513 K, a CO/H2 ratio of 1, and various space velocities in order to investigate the effect of the CO conversion level on the product distribution. The catalytic properties of Ru/NaY prepared with ion-exchange method did not show any dependence on the CO conversion level. However, those prepared from ruthenium carbonyl did show significant changes even at low CO conversion. The results can be interpreted in terms of the high activity of Ru3(CO)12/NaY in the water-gas shift reaction.