Mukherjee, who was accompanied by Kerala Governor Sheila Dikshit, was received at the western portal of the grand complex by temple Executive Officer K N Satheesh and other officials.
He spent about 40 minutes in the temple before leaving for Tiruchirapally in Tamil Nadu.
Security was tightened in and around the sprawling temple complex.
The temple is one of the richest Hindu shrines with its underground vaults containing immense wealth.
Mukherjee had yesterday attended the convocation ceremony of Central University of Kerala at the northern district Kasargod and inaugurated the platinum jubilee celebrations of the College of Engineering here.