The VHP also described him as a role model for all, including Muslims, who it said should look up to him for the progress of the community and the country.
Expressing condolence over his demise, VHP's patron Ashok Singhal said Kalam was a "worthy son of the soil" whose elevation as President "dignified" the top office.
"We deeply condole the demise of Dr Kalam who earned the reputation of Missile Man; was world famous; who accomplished the mission of nuclear explosion at Pokhran so skillfully that no one in the world had a whiff of it; who prided in being called a teacher and who never hurt anyone. We are deeply pained at his sudden demise and offer our deepest condolences to his family," Singhal said in a statement.
"He (Kalam) was the only one who had received the 'Bharat Ratna' before assuming the office of President. He was active till his last breath," he said.
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"I pay may deepest condolences on behalf of the entire VHP family... May his soul rest in peace," Togadia said.
VHP joint general secretary Surendra Jain said Kalam was a person beyond the boundaries of any religion.
"But even if we consider him a Muslim, he is a role model for the Muslim society. Their role models cannot be Ghazni, Aurangzeb, Jinnah or leaders like Owaisi or Azam Khan.