Palakaad District Collector P Marykutty issued an order late last night stating that since the Karnagi Amman school was government-aided, only elected representatives or school authorities could hoist the flag, as per protocol.
The Rashtriya Swayamsevak Sangh (RSS) said in a statement that after due consultations, "the school authorities decided that they would proceed as planned and that Bhagwat must exercise his constitutional rights".
"We condemn such brazen attempts by the CPI-M led government of Kerala to deny the basic citizen rights of celebrating Independence Day and their continuous attempts to poison the state of Kerala with divisive politics," RSS's Akhil Bharatiya Prachar Pramukh Manmohan Vaidya said.
The DC said the administration would take action in the matter.
"We will give instruction to the police to register a case," she said.
Bhagwat is in the state to take part in a two-day meeting of the Sangh which began here yesterday. The state has witnessed political violence involving activists from the ruling CPI(M) and the RSS.
Addressing the students, Bhagwat said, "It is our duty to remember the sacrifices and hard efforts of those who laid down their lives during the struggle for Independence. We have to bring that dedication to our lives".
Independence, he said, was "sacred". "We have to protect it," he added.
There has been a spike in recent times in clashes between the RSS and CPI(M) cadres, with each accusing the other of murdering their respective workers.