He offered 'Kadali Pazham' a small and sweet variety of banana, mainly grown for offerings to temples in the state and ghee to the presiding deity, temple officials said.
Mukherjee, who was accompanied by Kerala Governor P Sathasivam and Devaswom Minister V S Sivakumar, spent nearly half an hour at the shrine.
Heavy security arrangements had been made at the temple complex in view of his visit.
The President is scheduled to launch five key projects tomorrow including declaration of Kerala as the first digital state and dedication of the UL CyberPark to the nation.