The area of research to discover new Li containing materials and to understand their physical properties has been of constant interest due to applications potential for rechargeable batteries. Here, we present the results of magnetic investigations on a Li compound, Li3Ni2RuO6, which was believed to be a ferrimagnet below 80 K. While our neutron diffraction (ND) and isothermal magnetization (M) data support ferrimagnetism, more detailed magnetic studies establish that this ferrimagnetic phase exhibits some features similar to spin-glasses. In addition, we find another broad magnetic anomaly around 40–55 K in magnetic susceptibility (χ), attributable to cluster spin-glass phenomenon. Gradual dominance of cluster spin-glass dynamics with a decrease of temperature (T) and the apparent spread in freezing temperature suggest that the ferrimagnetism of this compound is a chaotic one. The absence of a unique freezing temperature for a crystalline material is interesting. In addition, pyroelectric current (Ipyro) data reveals a feature in the range 40–50 K, attributable to thermally stimulated depolarization current. We hope this finding motivates future work to explore whether there is any intriguing correlation of such a feature with cluster spin-glass dynamics. We attribute these magnetic and electric dipole anomalies to the crystallographic disorder, intrinsic to this compound.