The President flew to Kirnahar, 240KM from Kolkata, in a helicopter with his wife Subhra and spent around 20 minutes with his elder sister Annapurna Banerjee.
From Kirnahar, he drove the three kilometre distance to his ancestral house at Mirati where he would worship Durga as a priest from tomorrow.
The media were not allowed beyond the gate of Mukherjee's residence.
The President emerged later in the evening and said he would pray for the welfare of the people of the country during the puja.
Mukherjee said he would follow all the traditions that he has followed every year during the puja.
Earlier, in Kolkata he met Chief Minister Mamata Banerjee at the VIP lounge of Netaji Subhas Chandra Bose International Airport after arriving from Delhi by a special aircraft of the Indian Air Force.
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The President was received by Governor M K Narayanan, the chief minister and high officials.
He will leave for Delhi on October 23.