The sister, aged 72, was attacked by bandits as she tried to stop them stealing from a convent.
She is in critical condition after she was attacked when up to a dozen attackers broke in to the building at around 1am yesterday.
They tied up several nuns as they began to steal from the Convent of Jesus and Mary School, in Ranaghat, India.
The nun who was raped did not receive hospital treatment until the following morning, Sky News reports.
She was reportedly critically injured and required surgery.
Prayers were said at churches across India following the incident, which has added to protests over sexual violence against women in the country.
Father Dominic Gomes, Vicar General of Kolkata Archdiocese, told NDTV:
“After tying three of the five sisters, they entered the principal’s room and ransacked it, destroying property and taking money, a laptop and a mobile phone.”
An inquiry has been launched into the incident, West Bengal’s Chief Minister Mamata Banerjee said.
She said: “We strongly condemn the incident that took place at the Ranaghat Convent. CID will be examining all aspects to this horrific crime. Swift, strongest action to be taken.”
Rape has become a massive social problem in India, with growing calls for the Government to do more to help prevent it.
It comes after an Indian TV channel which was due to air a BBC documentary about the country’s rape crisis halted programming in protest at the banning of the film.
Instead of rescheduling another programme, the NDTV Channel ran a slate referring to the film’s title, during the hour-long slot when it should have aired.
The film features the horrific story of murdered gang-rape victim Jyoti Singh, 23, who became known as ” India’s Daughter” – the title of the documentary.
Jyoti, a medical student, was raped and killed by a gang of men on a public bus in December 2012.
The documentary made by British filmmaker Leslee Udwin features an interview with Mukesh Singh, one of the men convicted of the appalling crime on a Delhi bus, and was outlawed by the Indian authorities on the grounds of “objectionable content” amid claims it was offensive to women.