The Jangipur MP met Prasad at the Birsa Munda Central Jail in Ranchi on Sunday.
A Central Bureau of Investigation court had on September 30 awarded prison sentences to Prasad and 44 others for fraudulent withdrawal of Rs 37.7 crore from the Chaibasa treasury when he was at the helm of affairs in Bihar in the 1990s.
Prasad is scheduled to file an appeal in the Jharkhand high court on October 17 against the sentence passed by a special CBI court.
Mukherjee, who was going to Rajrappa also met Jharkhand Chief Minister Hemant Soren.