He will hoist the flag on January 26 in a school on the outskirts of Palakkad, RSS members said.
Bhagwat will be in Kerala to attend a three-day Rashtriya Swayamsevak Sangh (RSS) camp, to be held in a school near Palakkad town from January 26.
"The sarsanghchalakji (RSS chief) always hoists the national flag on Independence Day and Republic Day wherever he is on these days. Since on January 26 he will be in Kerala, he will hoist the flag there. It should only be seen in this light," a senior Sangh functionary said.
"There will be a programme on the morning of January 26 to mark and celebrate Republic Day, when sarsanghchalakji will unfurl the national flag," RSS's state coordinator KK Balram told PTI.
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Balram said there was no need to take permission from the local administration as the event was being organised in a Sangh-run school and not in a government institute.
Bhagwat had unfurled the tricolour at a government-aided school in Palakkad district on August 15 last year, flouting an order of the district administration. The state government has ordered action against the school authorities.
The state has been witnessing incidents of political violence involving cadres of the ruling Communist Party of India (Marxist) and the RSS.