According to authorities of the local convent school in Ranaghat sub-division, three-four people broke into the building at around 12:30 am and raped her after gagging her.
They also decamped with Rs 12 lakh kept in the locker of the cupboard after raping the nun.
The nun was taken to Ranaghat Hospital by the school hostel authorities in the morning when the matter came to light.
Chief Minister Mamata Banerjee ordered a CID probe into the incident and promised "swift" and "strongest action" against the culprits.
She said religious politics was being practised in the name of ghar wapsi and that religious fanaticism is on the rise.
"We strongly condemn the incident that took place at the Ranaghat Convent," she said.
"We have ordered a CID probe. The agency will be examining all aspects of this horrific crime. Swift, strongest action to be taken against the culprits," Banerjee added.
A CCTV footage of the building showed three persons who are suspected to be the rapists. Police is investigating.
District Magistrate P B Salim, who rushed to the spot, told PTI it was a heinous act and police were already on the lookout for the gang members. "We are yet to get a full picture of the incident," the DM said.
Aggrieved guardians of students blocked the arterial NH 34 and Sealdah-Ranaghat rail tracks from 12 noon as the news spread like wildfire in the locality.
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