In 2010, Central Bureau of Investigation investigated the fraudulent withdrawal of Rs 6.58 crore from the provident fund accounts of class III and IV employees in the Ghaziabad district court implicated members of higher judiciary, including Chatterjee. The report submitted by the Central Bureau of Investigation officials was examined by a bench comprising justices D. K. Jain, V. S. Sirpurkar, and G. S. Singhvi. Chatterjee denied the allegations.
Chatterjee married Kumkum Chatterjee. Their son Aniruddha Chatterjee is a practicing advocate of Calcutta High Court. Chatterjee died on 8 July 2023, at the age of 78.