Surendra Jain, the General Secretary, also denies that the attack was religiously motivated. According to The Times newspaper, he said: "It is a Christian culture to exploit nuns. We don't do such things."
His organisation, the World Hindu Council, is affiliated to Indian Prime Minister Narendra Modi's ruling Bharatiya Janata Party.
Narendra Modi's government has been accused of not doing enough to protect religious minorities. Mr Modi has said he is "deeply concerned" about the attack on the nun in her 70s, and has ordered an immediate report into the matter.
During the attack it is claimed eight men broke into the convent and Christian school in West Bengal. They raped the woman, destroyed objects and robbed the building.
The police have detained people for questioning, but it is reported no one has been formally arrested yet.
The Indian feminist writer and publisher Urvashu Butalia has said the attackers targeted the convent and school because it is Christian.
Large protests have been held across India, with both Christians and Hindus calling for better protection for religious minorities.
