The state's CPI(M)-led LDF government issued a circular yesterday laying the guidelines for hoisting the national flag on Republic Day in government and educational institutions.
According to the circular, heads of educational institutions have been asked to hoist the tricolour accompanied by the singing of the national anthem.
On Independence Day last year, Bhagwat had kicked up a row by hoisting the national flag at Karnakiamman higher secondary school, a government-aided institution, flouting an order by the Palakkad collector.
"This is not a government or aided school. The school management will decide who has to hoist the flag," RSS's state coordinator K K Balram told PTI.
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"The government circular is not binding on us as it is a private school," he added.
Bhagwat is visiting Kerala to attend a three-day camp of RSS workers at the school and there is nothing wrong in his hoisting the tricolour, he said.
Bhagwat, who will reachi Kochi tomorrow, will immediately leave for Palakkad, he added.